A letter from the Bureau of Internal Revenue (BIR) saying you are under audit is stressful. But a BIR audit follows a fixed legal sequence, and almost every step has a deadline that protects you as much as it binds you. Owners who know the sequence make better decisions, keep their rights and usually pay less.

This guide is for owners, finance managers and in-house accountants of Philippine businesses who have received, or expect, an audit notice. It walks you through every notice the BIR can send, from the electronic Letter of Authority (eLA) to warrants of garnishment. You'll get the deadlines for each reply, the Supreme Court rulings that void defective assessments, how to write a protest that holds up, and a realistic budget.

It also reflects the 2025–2026 changes: the nationwide audit suspension under RMC 107-2025, its lifting in January 2026, and the new "one eLA per taxable year" audit program under RMO 1-2026 and RMO 22-2026. If you want to lower your chance of being picked in the first place, read our guide to common BIR audit red flags. To get ready for a live audit, use our LOA audit readiness checklist.

Key takeaways

  • No valid audit authority, no valid assessment. As of October 2026, RMO 22-2026 (August 24, 2026) says every audit needs a valid eLA, Tax Verification Notice (TVN) or Mission Order (MO), and any audit without one is "unauthorized." The Supreme Court voided assessments made without a proper LOA in Medicard v. CIR (G.R. No. 222743, April 5, 2017).
  • Generally one eLA per taxable year. Under the Single-Instance Audit Framework (RMO 1-2026, January 27, 2026), one eLA covers all tax types for a given year. Fraud cases, one-time transactions, tax clearances and business closures are exceptions.
  • You have 15 days to answer a Preliminary Assessment Notice (PAN). If you don't reply in time, you are "in default" and the BIR issues the Formal Letter of Demand and Final Assessment Notice (FLD/FAN) (RR 12-99, as amended by RR 18-2013).
  • You have 30 days from receipt to protest the FLD/FAN. Miss it and the assessment becomes final, executory and demandable (Section 228, Tax Code). If you ask for reinvestigation, you have 60 days from filing the protest to submit supporting documents.
  • The BIR has 180 days to decide your protest. You then have 30 days to go to the Court of Tax Appeals (CTA). The 30 days run from receipt of the Final Decision on Disputed Assessment (FDDA) or from the end of the 180 days, whichever route you choose. You can't use both.
  • The BIR normally has 3 years to assess. The period runs from the filing deadline, or from the actual filing date if you filed late. It stretches to 10 years from discovery for false or fraudulent returns or non-filing (Sections 203 and 222).
  • Penalties add up fast. Expect a 25% surcharge (50% for fraud) plus 12% annual interest. Micro and small taxpayers (gross sales under ₱20 million) get a 10% surcharge and 6% interest under the Ease of Paying Taxes (EOPT) Act and RR 6-2024.

Overview

A BIR audit has three phases: examination (the revenue officer reviews your books), assessment (the BIR formally demands deficiency tax and you dispute it), and collection or appeal (the BIR enforces payment, or a court reviews the assessment). The Tax Code sets the skeleton. Section 6 lets the Commissioner of Internal Revenue (CIR) authorize examinations. Section 13 lets a revenue officer examine taxpayers in the district under a Letter of Authority. Section 228 sets the protest rules, and Sections 205 to 217 cover collection.

Who does what

Office or courtRole in your auditWhat you receive from it
BIR Revenue District Office (RDO) or Large Taxpayers Service (LTS)Issues the audit authority and examines your books through an assigned revenue officer (RO) and group supervisoreLA, checklist of requirements, Notice of Discrepancy, first and final requests for documents
BIR Regional Office (Assessment Division) or LTSReviews the audit report and issues assessment notices; decides protests as the CIR's authorized representativePAN, FLD/FAN, FDDA, termination letter
BIR Regional or National Investigation Division (RID or NID)Handles fraud cases, which may span several yearseLA or MO for fraud audits
Office of the CommissionerDecides administrative appeals from the authorized representative's FDDACommissioner's decision
BIR Collection DivisionEnforces final assessmentsCollection letter, Warrant of Distraint and/or Levy (WDL), Warrant of Garnishment
Court of Tax Appeals (CTA) DivisionHears your petition for review of the assessmentDecision; may suspend collection with a deposit or bond
CTA En BancReviews CTA Division rulingsEn banc decision
Supreme CourtFinal review on questions of lawFinal decision

The audit notices and what each one means

NoticeWhat it meansWhat you should do
Electronic Letter of Authority (eLA) or Letter of Authority (LOA)Authority for a named RO to fully examine your books for specific tax types and periods. Since RMO 1-2026 it must be labeled "Full Examination of Books of Accounts and Other Accounting Records"Verify it with the REVIE LOA Verifier. Check your name, TIN, taxable year, tax types and the named RO and group supervisor. Choose the audit venue on the consent form
Tax Verification Notice (TVN)Still in use. Limited authority to verify one specific transaction or claim, such as a refund. It is labeled "Verification Authority – Limited Scope"Give only what relates to that transaction. Broader questions need a separate eLA (RMC 14-2026)
Mission Order (MO)Limited authority for verification, surveillance, monitoring and inspection, such as checking invoices or registration. It is not authority for a full auditCooperate with the inspection. A full audit needs a separate eLA
Letter Notice (LN)A data-matching notice. Your returns don't match third-party data, such as your customers' and suppliers' reportsReconcile and reply. An LN alone can't support an assessment, but ignoring a data-matching request is now a ground for a mandatory eLA under RMO 22-2026
Notice for Informal Conference (NIC)No longer used. It was replaced by the Notice of Discrepancy under RR 22-2020Not applicable
Notice of Discrepancy (NOD)The RO's findings before any assessment. It is not yet an assessmentExplain your side within 5 days. The discussion may run up to 30 days from receipt
Preliminary Assessment Notice (PAN)The proposed assessment, stating the facts and lawReply within 15 days of receipt
Formal Letter of Demand and Final Assessment Notice (FLD/FAN)The actual assessment and demand for payment, with a due datePay, or file a protest within 30 days of receipt
Final Decision on Disputed Assessment (FDDA)The BIR's decision on your protestAppeal to the CTA, or to the Commissioner, within 30 days of receipt
Preliminary Collection Letter (PCL) and Final Notice Before Seizure (FNBS)Collection reminders on a final assessment. Under RMO 35-2019 the BIR may skip them and go straight to a warrantPay, or confirm that a timely protest or appeal is on file
Warrant of Distraint and/or Levy (WDL)Seizure of personal property (distraint) or real property (levy) for a delinquent taxAct immediately. Get legal advice on whether the assessment was ever final
Warrant of GarnishmentOrders third parties, usually your bank, to hold and turn over your fundsSame as the WDL

An audit is not an assessment. You owe nothing extra until a valid FLD/FAN is issued and becomes final, or a court upholds it. But every notice before that starts a clock you must respect.

What changed in 2025 and 2026

  • November 24, 2025: RMC 107-2025 suspended all field audits and the issuance of LOAs, MOs and TVNs nationwide. RMC 109-2025 (December 12, 2025) clarified the exceptions, such as cases prescribing within six months, one-time transactions, business retirements and refund claims.
  • January 27, 2026: RMC 8-2026 lifted the suspension. RMO 1-2026 introduced mandatory labels on audit instruments and the Single-Instance Audit Framework.
  • March 4, 2026: RMO 6-2026 and RMC 14-2026 set consolidation deadlines. All pending eLAs for the same taxpayer and year were consolidated from May 18, 2026. They also confirmed that a Replacement eLA for a reassigned RO is valid.
  • August 24, 2026: RMO 22-2026 consolidated the audit program. It splits cases into Mandatory Cases (fraud indicators, tax clearances for retiring businesses above ₱3 million in sales or ₱8 million in assets, refund claims, ignored data-matching requests) and Priority Cases. Priority Cases are picked by the system using risk criteria, such as input VAT above 75% of output VAT, income tax below 2% of gross sales, or no audit in more than five years of operations. The audit completion targets remain 180 days for RDO cases and 240 days for Large Taxpayer cases from the eLA date, first set in RMC 82-2022.
  • January 23, 2026: RMC 5-2026 added an LOA Verifier to the BIR's REVIE chatbot, so you can confirm an eLA is genuine before you hand over records.

Timeline

Here is how a regional audit typically unfolds in calendar days, from service of the eLA to the CTA appeal window. It assumes a request for reinvestigation and a BIR that uses its full decision period.

Typical BIR audit and dispute timeline (calendar days)
  1. eLA served with checklist and venue consent1–10Submit documents within 10 days of the request
  2. Follow-up requests for documents11–30First notice, then second and final notice, 10 days apart
  3. Examination by the revenue officer1–180180-day target for regional cases; 240 for LTS
  4. Notice of Discrepancy and discussion150–1855 days to explain; discussion capped at 30 days
  5. Review and issuance of PAN185–240Varies by office (estimate)
  6. Reply to PAN240–25515 days from receipt
  7. FLD/FAN issued255–270Due within 15 days of your PAN reply; late issue alone does not void it
  8. Protest window270–30030 days from receipt of the FLD/FAN
  9. Supporting documents for reinvestigation300–36060 days from filing the protest
  10. BIR decision period360–540180 days from submission of documents
  11. CTA appeal window540–57030 days from FDDA or from the end of the 180 days

Scale: calendar days

This timeline assumes complete documents and prompt service of each notice. Real audits often run longer because of follow-up requests, RO reassignment, waivers of the prescriptive period and review backlogs. The order is fixed by law, but the length varies by office and case.

The audit and dispute flowchart

BIR audit, assessment and appeal process
  1. eLA servedThe BIR authorizes named revenue officers to examine specific tax types and yearsCheck the taxpayer name, TIN, period, tax types and named RO. An audit without a valid eLA is void (Medicard, Sony)
  2. Request for documentsThe RO lists the books, returns and schedules neededSubmit within 10 calendar days. Non-compliance leads to a first notice, a final notice, then a subpoena duces tecum
  3. Examination and Notice of DiscrepancyThe RO tests your records and presents findings in a Notice of DiscrepancyExplain within 5 days; discussion up to 30 days. If resolved, you get a termination letter
  4. Preliminary Assessment Notice (PAN)The BIR proposes a deficiency assessment with facts and lawReply within 15 days. No reply means default, and the FLD/FAN follows
  5. FLD/FANThe BIR formally assesses and demands payment with a due datePay, or protest within 30 days. No valid protest means the assessment is final, executory and demandable
  6. ProtestYou file a request for reconsideration or reinvestigationFor reinvestigation, submit all supporting documents within 60 days of filing or the assessment becomes final
  7. FDDA or inactionThe BIR decides within 180 daysIf denied, go to the CTA or the Commissioner within 30 days. If the BIR doesn't act, appeal within 30 days after day 180 or wait for the decision
  8. CTA DivisionYou file a petition for reviewCollection is not suspended unless the CTA orders it, with a cash deposit or surety bond of up to double the amount
  9. CTA En Banc and Supreme CourtFurther review of adverse rulingsMotion for reconsideration with the Division first, then the En Banc within 15 days, then the Supreme Court under Rule 45
  10. CollectionThe BIR enforces a final assessment by warrantWarrants of distraint, levy and garnishment can reach property and bank accounts. RMO 35-2019 lets the BIR skip the PCL and FNBS

Requirements

What the BIR asks for depends on the tax types and years in the eLA. The checklist served with the eLA is the controlling list. Use this as a baseline, and see our LOA audit readiness checklist for a fuller version.

To answer the eLA

  • [ ] Certified copy of the eLA and the checklist of requirements
  • [ ] Signed Taxpayer's Consent on Audit Venue and Authorized Representative (RMO 22-2026 annex). Choose your office or the BIR office
  • [ ] Special power of attorney (individuals) or board resolution or secretary's certificate (corporations) naming your representative
  • [ ] BIR Certificate of Registration (Form 2303) and any updates
  • [ ] Registered books of accounts: general journal, general ledger, sales and purchase books, cash receipts and disbursements books (manual, loose-leaf or computerized)
  • [ ] Filed returns for the period, with proof of payment: income tax, VAT or percentage tax, withholding taxes, and documentary stamp tax if applicable
  • [ ] Audited financial statements and the Annual Income Tax Return (corporations and individuals required to file audited statements)
  • [ ] Alphalists, summary lists of sales and purchases (VAT taxpayers), and Certificates of Creditable Tax Withheld at Source (BIR Form 2307)
  • [ ] Sales invoices, supplier invoices, contracts, bank statements and payroll records, as requested
  • [ ] Reconciliations: revenue per books against returns, and VAT and withholding tax per returns against the general ledger

To answer the Notice of Discrepancy and PAN

  • [ ] Point-by-point written reply to each finding
  • [ ] Schedules and reconciliations that support each disputed item
  • [ ] Third-party confirmations (customer statements, supplier certifications) for data-matching differences
  • [ ] Proof of the date you received each notice: envelope, registry return card or receiving stamp

To protest the FLD/FAN

  • [ ] Protest letter stating that it is a request for reconsideration or reinvestigation, the date of the assessment notice, and the facts, law, rules and jurisprudence for each disputed item
  • [ ] List of the new or additional evidence you'll present (reinvestigation only)
  • [ ] Proof of payment for any items you accept
  • [ ] Proof of filing: receiving copy or registry receipt

For a CTA appeal

  • [ ] Verified petition for review, with certified copies of the FLD/FAN, protest, FDDA (if any) and proof of receipt dates
  • [ ] Docket and filing fees
  • [ ] Where you seek suspension of collection: a motion and a cash deposit or surety bond, as the CTA requires

Step-by-step procedure

Step 1: Check the eLA before anything else

When the eLA is served, first confirm it is genuine. Use the LOA Verifier in the BIR's REVIE chatbot, launched under RMC 5-2026 (January 23, 2026). Then read it carefully. Check your name, TIN, the tax types, the taxable period and the named RO and group supervisor. In CIR v. Sony Philippines (G.R. No. 178697, November 17, 2010), an LOA for "1997 and unverified prior years" could not support an assessment based on early-1998 records. The Court called that examination a nullity. In CIR v. McDonald's Philippines Realty (G.R. No. 242670, May 10, 2021), an RO who replaced the officer named in the LOA, without a new LOA, had no authority. Today the BIR handles reassignments with a Replacement eLA (RMC 14-2026).

  • Where: Served at your registered address. You'll also sign the venue and representative consent.
  • What you get: A defined audit scope.
  • Timing: Gather documents right away. The first request gives 10 calendar days.
  • Forms: eLA, the standard Checklist of Requirements (Annex B of RMO 1-2026) and the consent form (RMO 22-2026).

If you question a Replacement eLA, the audit keeps going while you do. RMC 14-2026 says such a challenge doesn't suspend the audit.

Older LOA timing rules are contested. RMO 43-90 required service of an LOA within 30 days of issue. RMC 82-2022 (June 30, 2022) says that rule was removed and that late service is not a ground to refuse an eLA. The same circular set audit completion targets of 180 days for RDO cases and 240 days for Large Taxpayer cases, counted from the eLA's issue date. The CTA continues to litigate this, so ask your adviser before you rely on it.

Step 2: Submit documents and track every request

Submit what the checklist asks for and keep a transmittal log. Under RMO 22-2026, if you don't submit, a First Notice follows after 10 calendar days and a Second and Final Notice after another 10. Continued non-compliance can lead to a subpoena duces tecum, and failing to obey one can mean criminal charges. Once a valid subpoena is issued, you lose the right to choose the audit venue. Certified photocopies are generally accepted. Originals are needed only for verification.

  • Where: Your office or the BIR office, as chosen on the consent form.
  • Timing: 10 calendar days per request.

Step 3: Respond to the Notice of Discrepancy

When the RO finishes, you get a Notice of Discrepancy listing the findings. Under RR 22-2020 you have 5 days to explain your side, and the discussion may run up to 30 days from receipt. Ask for minutes of each meeting. RMO 22-2026 prescribes a Minutes of Discussion form signed by both sides. If the issues are resolved or you pay, the case closes with a termination letter. If not, the case goes for review and PAN issuance within 10 days after the discussion ends.

Step 4: Reply to the PAN within 15 days

The PAN must show "in detail the facts and the law" behind the proposed assessment (RR 18-2013, Section 3.1.1). Reply in writing within 15 days of receipt, and dispute each item with documents. If you don't, you're in default and the FLD/FAN follows. If you reply, the FLD/FAN is due within 15 days of your reply. RMO 22-2026 says a late FLD/FAN is not void for that reason alone, as long as it is issued within the prescriptive period and due process is observed.

Section 228 lists five cases where no PAN is needed. Examples are a mathematical error on the face of the return, and withholding tax that was withheld but not remitted. In those cases the FLD/FAN comes directly.

Step 5: Decide on the FLD/FAN and protest within 30 days

The FLD/FAN is the assessment. It must state the facts, law, rules and jurisprudence it relies on, or it is void (Section 228; RR 18-2013, Section 3.1.3). It must also demand a definite amount by a definite date. In CIR v. Fitness by Design (G.R. No. 215957, November 9, 2016), a notice whose amount "will have to be adjusted" and whose due date was unclear was not a valid assessment. The warrant based on it was void.

You then choose:

  • Pay the items you accept. Undisputed items become final immediately anyway.
  • Request reconsideration: the BIR re-evaluates using the existing records. There's no 60-day document period.
  • Request reinvestigation: the BIR re-evaluates using new or additional evidence. You must submit all relevant supporting documents within 60 days of filing the protest, or the assessment becomes final.

Step 6: Wait for the FDDA, or act on inaction

The BIR has 180 days to decide. For reconsideration, the 180 days run from filing. For reinvestigation, they run from the submission of documents. The FDDA must state the facts and law and say that it is the final decision, or it is void (RR 18-2013, Section 3.1.5).

  • If an authorized representative (for example, a Regional Director) denies your protest: appeal to the CTA within 30 days of receipt, or elevate a request for reconsideration to the Commissioner within 30 days. No new reinvestigation is allowed at that stage.
  • If the Commissioner denies it: appeal to the CTA within 30 days. A motion for reconsideration does not stop the 30-day clock.
  • If no decision comes within 180 days: appeal to the CTA within 30 days after day 180, or wait for the decision and appeal within 30 days of receiving it. Lascona Land Co. v. CIR (G.R. No. 171251, March 5, 2012) confirmed that these options are "mutually exclusive." Choosing one bars the other.

Step 7: Appeal to the Court of Tax Appeals

File a petition for review with a CTA Division within 30 days (Section 11, RA 1125 as amended by RA 9282). Filing does not automatically stop collection. The CTA may suspend collection if it would jeopardize the government's or your interests. It may require a cash deposit or a surety bond of up to double the amount. If you lose at the Division, file a motion for reconsideration. Then you can go to the CTA En Banc by petition for review within 15 days of receiving the resolution (Rule 8, Revised Rules of the CTA). After that, you can file a Rule 45 petition with the Supreme Court within 15 days.

Step 8: Handle collection

An assessment becomes final, executory and demandable if you don't protest within 30 days, don't submit reinvestigation documents within 60 days, or don't appeal within 30 days. At that point, Sections 205 and 207 let the BIR distrain personal property, including bank accounts, and levy on real property. The Commissioner's authorized representative acts on amounts above ₱1 million. The RDO acts on ₱1 million or less. Distraint and levy can't be used where the tax is ₱100 or less. Distraint and levy may be repeated until the full amount is collected (Section 217).

Estimated costs and budget

These figures are as of October 2026. Statutory rates are cited. Professional and court costs are estimates that vary with the size of the assessment, the number of issues and the adviser.

ItemAgencyEstimated cost (₱)Notes or basis
Deficiency taxBIRVariesThe basic tax found due
Surcharge, regular taxpayersBIR25% of the deficiencySection 248(A), as amended by RA 11976
Surcharge, fraud or willful neglect to fileBIR50% of the deficiencySection 248(B). It still applies to micro and small taxpayers
Surcharge, micro and small taxpayersBIR10% of the deficiencySection 45(b), RA 11976; RR 6-2024. Applies to gross sales under ₱20 million
Interest, regular taxpayersBIR12% a yearSection 249: double the legal interest rate set by the Bangko Sentral ng Pilipinas (BSP). Deficiency and delinquency interest are not charged at the same time
Interest, micro and small taxpayersBIR6% a year50% reduction under Section 45(c), RA 11976; RR 6-2024
Compromise penaltyBIRPer RMO 7-2015 schedulePaid instead of criminal prosecution, by agreement. It is 50% lower for micro and small taxpayers (RR 6-2024)
Notarization of protest papers, SPAs and secretary's certificatesNotary public500–3,000Estimate; varies by city
Professional fees, audit support to FLD/FANPrivate50,000–300,000Estimate for a small or medium company; depends on years, tax types and issues
Professional fees, protest and reinvestigationPrivate50,000–250,000Estimate
CTA docket and filing feesCTA5,000–100,000Estimate. Based on the amount in dispute; confirm with the CTA docket section
Legal fees, CTA litigationPrivate300,000–1,500,000+Estimate; multi-year litigation
Surety bond premium, if you seek suspension of collectionBonding companyVariesBond of up to double the amount assessed (RA 9282). The premium is a percentage of the bond
Total, excluding deficiency tax, surcharge and interestAbout 100,000–2,000,000Estimate. The low end is settled at BIR level; the high end goes to the CTA

Budget to prepare. Separate three buckets. Government amounts are the deficiency tax, surcharge, interest and any compromise penalty. They are set by law and keep growing while unpaid, so paying the items you accept early limits interest. Court costs are CTA docket fees and any bond, needed only if you appeal. Optional costs are notarization and professional fees. Good representation at the PAN stage is usually the cheapest money you'll spend, because issues dropped before the FLD/FAN never need a protest.

Prescription and waivers

The three-year assessment period in Section 203 is your strongest defense against old assessments. It runs from the last day to file the return, or from the actual filing date if you filed late. For false or fraudulent returns or non-filing, Section 222(a) allows 10 years from discovery. Fraud must be alleged in the assessment and proven, as Fitness by Design stressed. Section 223 suspends the clock in some situations, such as when the BIR grants your request for reinvestigation or can't locate you at your registered address.

The BIR often asks for a waiver of the statute of limitations to extend the period. Under Section 222(b), it must be signed before the period expires. RMO 14-2016 (April 4, 2016) relaxed the old RMO 20-90 formalities. A waiver is now valid if it states its date of execution, is signed by you or a responsible official, and states the new expiry date. RMO 14-2016 also puts the burden of proper execution on the taxpayer. The courts look closely at waivers:

  • CIR v. Kudos Metal Corp. (G.R. No. 178087, May 5, 2010) voided waivers signed by an unauthorized accountant without a notarized authority, with no date of BIR acceptance. The assessments were time-barred.
  • Asian Transmission Corp. v. CIR (G.R. No. 230861, September 19, 2018) upheld defective waivers against a taxpayer who benefited from them. The taxpayer "has the primary responsibility for the proper preparation of the waiver."

Don't sign a waiver by reflex. A waiver gives the BIR more time to assess you. Sign one only when you need more time to gather documents, and keep it limited to the taxes and period under audit.

Due process and void assessments

Section 228 says the taxpayer "shall be informed in writing of the law and the facts on which the assessment is made; otherwise, the assessment shall be void." The Supreme Court has enforced this strictly:

CaseDefectResult
Medicard Philippines v. CIR, G.R. No. 222743, April 5, 2017Assessment based on a Letter Notice, with no LOAVoid. The Court said it "cannot convert the LN into the LOA required under the law"
CIR v. Sony Philippines, G.R. No. 178697, November 17, 2010Examination of a period not covered by the LOAAssessment for that period void
CIR v. McDonald's Philippines Realty, G.R. No. 242670, May 10, 2021Substitute RO with no new LOAVoid. Naming the RO is a jurisdictional requirement
CIR v. Fitness by Design, G.R. No. 215957, November 9, 2016FAN with no definite amount or due dateNot a valid assessment. The warrant was void
CIR v. South Entertainment Gallery, G.R. No. 223767, April 24, 2023FLD not shown to have been validly served by registered mailVoid. The FNBS and WDL fell with it

The lesson for you: document everything. Keep the envelopes, registry cards and receiving stamps for every notice. Many winning defenses depend on exactly when, or whether, a notice was received.

When to protest and how

Protest when you have a factual or legal basis to dispute an item and the amount justifies the cost. Pay items you agree with. Undisputed items become final anyway, and paying them stops interest.

What your protest letter must contain (RR 18-2013, Section 3.1.4). Without the first three items, the protest is "void and without force and effect":

  1. The nature of the protest: reconsideration or reinvestigation. For reinvestigation, list the new or additional evidence you'll present.
  2. The date of the assessment notice you are protesting.
  3. The applicable law, rules, regulations or jurisprudence for each issue. An issue raised without facts and law is treated as undisputed and becomes final.
  4. A clear computation of what you believe is the correct tax, item by item.
  5. Your request: cancel or reduce the assessment, and lift penalties where there's a basis.

What to attach: the FLD/FAN and its details of discrepancies, proof of receipt date, your authority to sign (board resolution or SPA), payment proof for accepted items, and the supporting schedules you already have.

Common fatal mistakes

  • Missing the 30-day protest window. Count from receipt of the FLD/FAN, not its date. A late protest can't revive a final assessment.
  • Protesting the PAN only. A reply to the PAN is not a protest of the FLD/FAN. You must protest again after the FLD/FAN arrives.
  • Choosing reinvestigation and then not submitting documents within 60 days. The assessment becomes final on the documents you failed to give.
  • Filing a motion for reconsideration of the Commissioner's denial instead of going to the CTA. It does not stop the 30-day appeal period.
  • Mixing the inaction options. After 180 days you either appeal within 30 days or wait for the decision. Waiting a while and then filing late loses both.
  • Filing the protest with the wrong office. File with the office that issued the FLD/FAN, and keep proof of filing.
  • Ignoring a Letter Notice or data-matching request. Under RMO 22-2026, failing to respond to third-party data matching is itself a ground for a mandatory eLA.

Frequently asked questions

Can the BIR garnish my bank account?

Yes, but only to collect a delinquent tax, usually after the assessment has become final, executory and demandable or a court has upheld it. Sections 205 and 207 of the Tax Code include bank accounts among the property the BIR can distrain through a warrant of garnishment served on your bank. RMO 35-2019 lets the BIR issue a warrant without first sending a Preliminary Collection Letter and Final Notice Before Seizure. If a warrant arrives while a protest or appeal is pending, get legal help right away.

What happens if I ignore a PAN?

You are treated as in default after 15 days, and the BIR issues the FLD/FAN for the full proposed amount plus penalties (RR 18-2013). You can still protest the FLD/FAN within 30 days of receipt. But you'll have lost a cheap chance to resolve the issues before a formal assessment, and the findings will be harder to reverse.

How long can a BIR audit take?

The BIR's internal targets are 180 days for RDO and regional cases and 240 days for Large Taxpayer cases from the eLA date (RMC 82-2022, carried into RMO 22-2026). The audit period is suspended while the BIR waits on a subpoena or information request. Counting the PAN, FLD/FAN, protest and the BIR's 180-day decision period, a disputed case can easily run 18 months or more before it reaches the CTA. A CTA appeal can add several years.

Can the BIR audit the same year twice?

Generally no. Section 235 of the Tax Code allows only one examination of books for income tax purposes per taxable year. The exceptions include fraud, irregularities or mistakes, a reinvestigation you requested, and withholding tax or capital gains tax verification. Since January 2026, the Single-Instance Audit Framework also limits the BIR to one eLA per taxpayer per taxable year, covering all tax types, except in fraud and transaction-based cases.

How far back can the BIR assess?

Normally three years from the filing deadline, or from the actual filing date if you filed late (Section 203). For false or fraudulent returns or non-filing, it's 10 years from discovery (Section 222). A valid waiver can extend the period. Under the EOPT Act you must keep books and records for five years (Section 235, as amended by RA 11976).

Should I request reconsideration or reinvestigation?

Choose reconsideration if your records already prove your position and the dispute is mainly about the law or the BIR's reading of the records. There's no 60-day document deadline. Choose reinvestigation if you need to present new or additional evidence, and be ready to submit everything within 60 days of filing.

How Upcloud can help

We represent businesses through every stage of a BIR audit. We check the eLA, organize document submissions, answer the Notice of Discrepancy and PAN, and prepare protests with the right legal and factual support. Learn more about our tax compliance services and other services. If you've just received an audit notice, contact us so we can review your deadlines with you.

References

  1. Bureau of Internal Revenue. Revenue Memorandum Order No. 22-2026 (Digest): Consolidated and revised policies, guidelines and procedures for the BIR Audit Program. August 24, 2026. https://bir-cdn.bir.gov.ph/BIR/pdf/RMO%20No.%2022-2026%20Digest.pdf
  2. Bureau of Internal Revenue. Revenue Memorandum Order No. 1-2026 (Digest): Revised policies, controls and procedures for tax audit and assessment. January 27, 2026. https://bir-cdn.bir.gov.ph/BIR/pdf/RMO%20No.%201-2026%20Digest.pdf
  3. Bureau of Internal Revenue. Revenue Memorandum Circular No. 8-2026 (Digest): Resumption of tax audit and field operations. January 27, 2026. https://bir-cdn.bir.gov.ph/BIR/pdf/RMC%20No.%208-2026%20Digest.pdf
  4. Bureau of Internal Revenue. Revenue Memorandum Circular No. 14-2026 (Digest): Clarifications on RMC 8-2026, RMO 1-2026 and RMO 6-2026. March 4, 2026. https://bir-cdn.bir.gov.ph/BIR/pdf/RMC%20No.%2014-2026%20Digest.pdf
  5. Bureau of Internal Revenue. Revenue Memorandum Circular No. 5-2026 (Digest): LOA Verifier in the BIR chatbot REVIE. January 23, 2026. https://bir-cdn.bir.gov.ph/BIR/pdf/RMC%20No.%205-2026%20Digest.pdf
  6. Bureau of Internal Revenue. Revenue Memorandum Circular No. 109-2025 (Digest): Coverage of the audit suspension under RMC 107-2025. December 12, 2025. https://bir-cdn.bir.gov.ph/BIR/pdf/RMC%20No.%20109-2025%20Digest.pdf
  7. Department of Finance. Statement on the immediate and temporary suspension of all Bureau of Internal Revenue field audits and related operations. November 24, 2025. https://www.dof.gov.ph/statement-of-finance-secretary-frederick-d-go-and-bureau-of-internal-revenue-commissioner-charlito-martin-r-mendozaon-the-immediate-and-temporary-suspension-of-all-field-audits-and-related-operation/
  8. Congress of the Philippines (via Lawphil). Republic Act No. 8424, National Internal Revenue Code of 1997 (Sections 6, 13, 203, 205–217, 222, 223, 228, 235). 1997. https://lawphil.net/statutes/repacts/ra1997/ra_8424_1997.html
  9. Congress of the Philippines (via Lawphil). Republic Act No. 11976, Ease of Paying Taxes Act (Sections 41 and 45). January 5, 2024. https://lawphil.net/statutes/repacts/ra2024/ra_11976_2024.html
  10. Congress of the Philippines (via Lawphil). Republic Act No. 10963, TRAIN Law (Section 75, amending Section 249 on interest). 2017. https://lawphil.net/statutes/repacts/ra2017/ra_10963_2017.html
  11. Congress of the Philippines (via Lawphil). Republic Act No. 9282, expanding the jurisdiction of the Court of Tax Appeals. 2004. https://lawphil.net/statutes/repacts/ra2004/ra_9282_2004.html
  12. Bureau of Internal Revenue (via Lawyerly). Revenue Regulations No. 18-2013, amending RR 12-99 on due process in deficiency tax assessments. November 28, 2013. https://lawyerly.ph/laws/view/l67487
  13. P&A Grant Thornton. Notice of Discrepancy to replace Notice of Informal Conference in tax assessments (RR 22-2020). September 18, 2020. https://www.grantthornton.com.ph/alerts-and-publications/technical-alerts/tax-alert/2020/notice-of-discrepancy-to-replace-notice-of-informal-conference-in-tax-assessments/
  14. P&A Grant Thornton. EOPT is here: revised rules on taxpayer classification and reduced penalties for micro and small taxpayers (RR 6-2024 and RR 8-2024). 2024. https://www.grantthornton.com.ph/insights/articles-and-updates1/tax-notes/eopt-is-here-revised-rules-on-taxpayer-classification-and-reduced-penalties-for-micro-and-small-taxpayers/
  15. Bureau of Internal Revenue (via P&A Grant Thornton). Revenue Memorandum Order No. 14-2016, guidelines for the execution of waivers of the defense of prescription. April 4, 2016. https://www.grantthornton.com.ph/globalassets/1.-member-firms/philippines/tax-alerts/2016/04.26.2016/rmo-14-2016.pdf
  16. Reyes Tacandong & Co. RMO No. 22-2026 and the institutionalization of BIR audit reform. 2026. https://www.reyestacandong.com/rmo-no-22-2026-and-the-institutionalization-of-bir-audit-reform/
  17. Forvis Mazars Philippines. BIR clarifies the 30-day submission of the electronic letter of authority (RMC 82-2022). 2022. https://www.forvismazars.com/ph/en/insights/tax-alerts/bir-rmc-82-2022
  18. MTF Counsel. Revisiting rules on warrant of distraint and/or levy (RMO 35-2019). February 11, 2021. https://mtfcounsel.com/2021/02/11/revisiting-rules-on-warrant-on-distraint-and-or-levy/
  19. Supreme Court (via Lawphil). Medicard Philippines, Inc. v. Commissioner of Internal Revenue, G.R. No. 222743. April 5, 2017. https://lawphil.net/judjuris/juri2017/apr2017/gr_222743_2017.html
  20. Supreme Court (via Lawphil). CIR v. Sony Philippines, Inc., G.R. No. 178697. November 17, 2010. https://lawphil.net/judjuris/juri2010/nov2010/gr_178697_2010.html
  21. Supreme Court (via Lawphil). CIR v. McDonald's Philippines Realty Corp., G.R. No. 242670. May 10, 2021. https://lawphil.net/judjuris/juri2021/may2021/gr_242670_2021.html
  22. Supreme Court (via Lawphil). CIR v. Fitness by Design, Inc., G.R. No. 215957. November 9, 2016. https://lawphil.net/judjuris/juri2016/nov2016/gr_215957_2016.html
  23. Supreme Court (via Lawphil). CIR v. South Entertainment Gallery, Inc., G.R. No. 223767. April 24, 2023. https://lawphil.net/judjuris/juri2023/apr2023/gr_223767_2023.html
  24. Supreme Court (via Lawphil). CIR v. Kudos Metal Corporation, G.R. No. 178087. May 5, 2010. https://lawphil.net/judjuris/juri2010/may2010/gr_178087_2010.html
  25. Supreme Court (via Lawphil). Asian Transmission Corporation v. CIR, G.R. No. 230861. September 19, 2018. https://lawphil.net/judjuris/juri2018/sep2018/gr_230861_2018.html
  26. Supreme Court (via Lawphil). Lascona Land Co., Inc. v. CIR, G.R. No. 171251. March 5, 2012. https://lawphil.net/judjuris/juri2012/mar2012/gr_171251_2012.html
  27. Court of Tax Appeals. Official website (rules, issuances and decisions). https://cta.judiciary.gov.ph/
Disclaimer. This article is general information, not tax, legal or accounting advice. Rules and rates change, so confirm the details for your business with a qualified adviser. Questions or corrections? Email [email protected].