Here’s a single, self-contained guide to the judicial settlement of an estate in the Philippines when the heirs missed the Estate Tax Amnesty—what that means, what happens next, and how to move forward. I’ll write this like a practical legal article (Philippine context, updated to TRAIN-era rules and the amnesty extension known before mid-2024), but not as a substitute for counsel on your specific facts.

What “missing the Estate Tax Amnesty” means

The Philippines enacted an Estate Tax Amnesty (originally under the 2019 Tax Amnesty Act and later extended). If you failed to file and pay within the amnesty window applicable to you, you simply lose the amnesty’s reduced penalties and simplified terms. You can still settle the estate—judicially or extrajudicially—but you are now under the regular estate tax regime with the usual surcharges, interest, and procedural steps.

In short: No amnesty ≠ no transfer. It just means you proceed under ordinary rules (and likely higher cost) until the estate is cleared and properties can be retitled.

Why judicial settlement (vs. extrajudicial)?

You use judicial settlement (a special proceeding in the Regional Trial Court) when any of the following is true:

There is a will that must be probated (letters testamentary to an executor).
There is no will but heirs disagree, or there are minors/incapacitated heirs, or the estate is indebted/complex, so the court’s supervision is prudent or required.
Titleholders, banks, or agencies refuse transfers absent a court order.
There are contested claims against the estate.

Extrajudicial settlement is faster and cheaper, but it requires a clean checklist (no minors, all heirs agree, no outstanding debts, etc.). If that breaks, you’re in court.

Core legal framework (ordinary, post-amnesty)

Estate tax rate: 6% of the net estate (TRAIN Law).
When to file: Generally within 1 year from death, but the BIR may grant extension to pay (see below). Missing that deadline triggers penalties but does not bar filing.
Where to file: BIR Revenue District Office (RDO) where the decedent was domiciled at death (or where the largest value of estate property is located, for non-resident cases with property in the Philippines).
Return used: BIR Form 1801 (Estate Tax Return); the estate must have its own TIN.
Transfer restrictions: Real property, shares, bank deposits, vehicles, etc., cannot be transferred/withdrawn until the BIR issues a Certificate Authorizing Registration (CAR / eCAR). The Registry of Deeds, corporate transfer agents, LTO, and banks will require this.

Judicial settlement: step-by-step

1) Open the special proceedings in the RTC

Venue: RTC of the province/city where the decedent resided at death (if non-resident: where any estate asset is situated).
Petitions:
- Probate (if there’s a will): to prove the will and appoint the executor named in the will.
- Intestate administration (if no will): to appoint an administrator.
Initial orders: Court issues Letters Testamentary/Administration. The executor/administrator (E/A) takes an oath and usually posts a bond (bond may be waived in a will for an executor).

2) Inventory, publication, and claims

The E/A must file a verified inventory and appraisal of the estate’s assets and liabilities within the court-set time.
Notice to creditors is published; a claims period runs for creditors to file claims against the estate. The E/A evaluates, admits or contests, and the court rules.

3) Estate tax compliance runs in parallel

Even while the case is pending, estate tax obligations accumulate. Typical track:

Secure TIN for the estate (BIR Form 1904).
Prepare the Estate Tax Return (BIR 1801):
- Asset schedule with values as of date of death:
  - Real property: use higher of zonal value or assessor’s FMV (or latest selling price if applicable).
  - Personal property: fair market values (bank balances as of death; listed shares at closing price; unlisted shares via book value; vehicles via book value or appraisals).
- Allowable deductions (TRAIN-era):
  - Standard deduction: ₱5,000,000.
  - Family home deduction: up to ₱10,000,000 (only the family home portion; any excess value is taxable).
  - Claims against the estate (valid debts existing at death; prove with notarized loan docs, statements, etc.; often BIR wants proof loan proceeds were received and used).
  - Unpaid mortgages/liens (with supporting security docs).
  - Losses (arising from casualty or theft within 6 months after death and not covered by insurance).
  - Vanishing deduction (property received by the decedent by donation/inheritance within 5 years and previously taxed).
  - Transfers for public use, and relevant allowable expenses actually incurred in settling the estate (e.g., court fees, publication, appraisals—keep receipts).
  - (TRAIN removed the old separate funeral/medical expense caps; do not rely on pre-TRAIN formulas.)
- Share of the surviving spouse in conjugal/community property is excluded (netting out before computing the decedent’s net estate).
Compute estate tax: 6% × (Net estate after deductions).
File and pay at the RDO; apply for CAR with full documentary set.

Penalties because the amnesty was missed

Surcharge: 25% for failure to file/pay on time (50% for willful neglect or false return).
Interest: Under the NIRC, interest equals double the legal interest rate set by the BSP (historically resulting in ~12% per annum in recent years), computed on the unpaid tax from the due date until full payment/assessment resolution.
Compromise penalties: Administrative amounts the BIR may impose in addition to surcharge/interest (varies by schedules).

Options to manage penalties/cash flow

Extension to pay (NIRC):
- Up to 5 years if the estate is under judicial settlement; up to 2 years if extrajudicial.
- Requires showing that payment on time would cause undue hardship; BIR may require a bond and set terms.
Installments: Often paired with an extension—BIR may allow staggered payments under conditions it sets.
Compromise or abatement (Sec. 204):
- Compromise (reduce basic tax) only if there is doubt as to validity of assessment or clear financial incapacity (documented).
- Abatement (reduce/cancel surcharges/interest) if imposition is unjust/excessive, or not the taxpayer’s fault, or cost of collection > amount due.
- These are discretionary—expect supporting evidence and time.
Bank withdrawals while CAR is pending: Banks generally hold deposits of the decedent unless presented with BIR authorization. There are rules that allow limited withdrawal subject to a final withholding on the amount withdrawn (admin practice evolved under TRAIN). Coordinate early with the RDO and the bank to avoid bottlenecks.

4) Paying debts, taxes, and expenses; partial distributions

The E/A liquidates assets, pays approved creditor claims, estate tax, and administration expenses following court oversight.
For liquidity, the court may authorize sales of assets or partial distributions if sufficient reserve remains for taxes, debts, and expenses.
Heirs should avoid off-the-record transfers while the CAR is pending; doing so risks void transfers and title defects.

5) Project of partition and court approval

When liabilities and taxes are settled or adequately provided for, the E/A submits a Project of Partition (how the estate will be divided), with valuations and any equalizing cash payments among heirs.
Court approval results in a Decree of Distribution.

6) Issuance of CAR and re-titling

With estate tax paid (or bonded per an approved extension/installment), and documents complete, the BIR issues the CAR/eCAR for each asset class.
Real property: Present CAR, Decree of Distribution (or probate order), tax clearances, and pay local transfer tax to the LGU; then process with the Registry of Deeds for new titles in the heirs’ names (or buyer’s name, if sold).
Shares of stock: Present CAR and court order to the corporate secretary/transfer agent to issue new certificates.
Vehicles: Present CAR and court order to the LTO for transfer.
Bank accounts: Present CAR and court order to the bank for release.

Documentary checklist (judicial path)

Expect the RDO and court to ask for many of the following (prepare early):

Court papers: Petition, Letters (Testamentary/Administration), Inventory/Appraisal, orders on claims, Project of Partition, Decree of Distribution.
Decedent documents: Death certificate, TIN (apply if none), marital regime evidence.
Heir documents: Valid IDs, TINs, birth/marriage certificates (to prove relationship).
Assets:
- Real property: Certified true copies of titles, latest tax declarations, real property tax clearances, location plans; zonal valuation references.
- Bank accounts: Bank certifications of balances as of date of death and account details.
- Shares/companies: Stock certificates, corporate secretary certifications, book value statements for unlisted shares.
- Vehicles: OR/CR.
Liabilities/deductions: Loan agreements, mortgage docs, statements of account; proof of use and existence at death; receipts for administration expenses.
Tax forms & receipts: BIR Form 1801, proof of payments, CAR application and checklist, documentary stamp proofs where applicable, LGU transfer tax receipts.

Computation primer (illustrative)

Assume the conjugal/community estate totals ₱40,000,000 at death; surviving spouse share is ₱20,000,000; so the gross estate of the decedent is ₱20,000,000. Deductions:

Standard deduction: ₱5,000,000
Family home portion within cap: ₱10,000,000 (if applicable to the decedent’s share)
Valid debts at death (proved): ₱1,500,000
Vanishing deduction (if qualified): ₱0 (assume none)

Net estate (illustrative): ₱20,000,000 − ₱5,000,000 − ₱10,000,000 − ₱1,500,000 = ₱3,500,000 Estate tax (6%): ₱210,000

If the one-year filing deadline was long missed, add 25% surcharge and interest (commonly ~12% p.a.) from the original due date until payment/assessment. If you secure an extension to pay or installments, compute interest per the approved schedule; consider abatement for surcharges/interest if facts justify.

Prescription/assessment risks when long overdue

If a return was filed, the BIR generally has 3 years from filing to assess (longer for false/fraudulent returns).
If no return was filed, the BIR may assess within 10 years from discovery of the omission. Practically, failing to file for years does not make the liability disappear; the clock runs from discovery, which can be triggered by any transaction involving estate assets (e.g., attempting to sell/transfer).
After assessment, the BIR typically has 5 years to collect administratively (longer if through court). Takeaway: Don’t wait for prescription—regularize the estate to avoid compounding costs and blocked transfers.

Practical strategies after missing amnesty

File now rather than wait. Interest compounds; land values (zonal) tend to rise; delay rarely helps.
Go judicial if needed (minors, disputes, debts). Court supervision protects the administrator from personal liability when acting under orders.
Ask for an extension/installments with a tight cash-flow plan and, if required, a bond.
Document deductions meticulously. The BIR is strict on claims against the estate—paper trail matters.
Consider selective asset sales with court approval to fund taxes/claims, rather than borrowing at high cost.
Explore abatement/compromise especially for surcharge/interest, when delays were due to factors beyond the heirs’ control or when the estate is genuinely illiquid.
Coordinate sequencing: Court orders ↔ BIR CAR ↔ LGU transfer tax/RPT ↔ Registries/banks/transfer agents. A misstep can send you back in line.

Frequent roadblocks (and how to pre-empt them)

Title defects (e.g., technical description issues, unregistered liens): Cure before CAR and ROD processing.
Unbooked family home evidence: Prove that the claimed property was the actual family home at death (barangay certs, utility bills, IDs).
Unsubstantiated debts: Notarization helps, but BIR wants contemporaneous proof (bank statements, vouchers, proof of proceeds).
Missing heirs/minors abroad: Court may require guardianship or special authority; secure apostilled/certified documents early.
Bank secrecy issues: Use formal administrator letters and court orders to obtain bank certifications.

Timeline & cost overview (ballpark, not promises)

Judicial proceedings: months to years, depending on disputes, court load, and completeness.
BIR CAR issuance: can be swift with complete, clean papers; can be lengthy if valuations are contested or documents are incomplete.
Professional fees: Court filing/publication, appraisal, survey, counsel, accountant, and notarial costs should be budgeted.

Quick FAQs

Q: Can we distribute before paying estate tax? A: Not validly. Transfers need CAR; registries and banks won’t process without it.

Q: We sold property years ago without CAR. What now? A: You’ll need to back-out regularization: settle estate tax, secure CAR, and then cure title transfers—sometimes with confirmatory deeds and additional taxes/penalties.

Q: Is probate always required because we missed amnesty? A: No. Amnesty status does not dictate judicial vs. extrajudicial. Facts of the estate (will, minors, disputes, debts) do.

Q: Can we still get any form of relief after missing amnesty? A: Possibly via extension to pay, installments, and abatement/compromise (discretionary) especially on surcharges/interest.

Action checklist (post-amnesty, judicial route)

Engage counsel and identify the proper RTC; prepare the petition (probate or intestate).
Apply for the estate’s TIN; start compiling a complete asset–liability inventory (as of date of death).
Draft the BIR 1801 with deductions supported by evidence; request extension/installments if needed.
Publish notice to creditors; resolve claims.
Pay estate tax / secure CAR (or bond per approved terms).
Submit Project of Partition; obtain Decree of Distribution.
Process transfers (ROD, LTO, banks, transfer agents) using CAR + court orders.
Close the estate after full accounting and distribution.

If you want, tell me the broad facts (date of death, with/without will, basic asset list, debts, minors/disputes, and which RDO the decedent fell under). I can map this into a tailored plan, a preliminary computation, and a document checklist you can hand to counsel and your RDO.