GSTR-9C Late Fee for FY 2025-26: When Does It Stop & How Is It Calculated?
Direct answer: If GSTR-9C is applicable for FY 2025-26, filing GSTR-9 alone does not complete the annual return under section 44. Under CBIC Circular No. 246/03/2025-GST, late fee under section 47(2) continues until the complete annual return is furnished — meaning GSTR-9 plus GSTR-9C where GSTR-9C is required. The fee is not a separate second late fee for GSTR-9C; it is one continuous annual-return late-fee computation up to the date the required GSTR-9C is filed.
Why this issue matters for FY 2025-26
Many finance teams still treat GSTR-9 and GSTR-9C as two independent year-end filings. That is risky. For taxpayers above the applicable GSTR-9C threshold, the annual-return compliance is not complete merely because GSTR-9 was filed on time. A delayed GSTR-9C can keep the section 47(2) late-fee clock running.
For FY 2025-26, the ordinary annual-return due date is 31 December 2026 unless extended by a later notification. Businesses that cross the GSTR-9C threshold should therefore plan GSTR-9 and GSTR-9C as one integrated closing process, not as sequential tasks separated by weeks.
CBIC clarification: one late-fee clock, complete annual return
CBIC Circular No. 246/03/2025-GST dated 30 January 2025 clarifies that where GSTR-9C is required, the annual return under section 44 is complete only when both GSTR-9 and GSTR-9C have been furnished. It further clarifies that late fee is not separately levied once for GSTR-9 and again for GSTR-9C. Instead, the late fee is calculated from the statutory due date until the date on which the complete annual return is furnished.
How the late-fee period works
Scenario 1 — GSTR-9C is not applicable: the late-fee period ends when GSTR-9 is furnished.
Scenario 2 — GSTR-9 and GSTR-9C are both applicable and both are filed together: the late-fee period ends on that filing date.
Scenario 3 — GSTR-9 is filed first and GSTR-9C is filed later: the late-fee period continues until the later GSTR-9C filing date, because the complete annual return has not been furnished before then.
Worked example for FY 2025-26
Assume a company is required to furnish GSTR-9C for FY 2025-26. It files GSTR-9 on 29 December 2026, before the ordinary 31 December due date, but files GSTR-9C on 10 January 2027. Based on CBIC’s clarification, the filing of GSTR-9 on 29 December does not complete the annual return. The relevant late-fee period runs from the due date until 10 January 2027. The exact monetary amount depends on the applicable section 47(2) rate and turnover-linked cap.
The GST Portal’s official FAQ uses the same principle: where GSTR-9 is filed before the due date but GSTR-9C is filed later, the system computes late fee for the delayed GSTR-9C period.
Is there a separate penalty for late GSTR-9C?
The key distinction is between late fee and other consequences. Circular 246 clarifies that section 47(2) late fee is for delay in furnishing the complete annual return; it is not levied twice merely because two forms are involved. However, inaccurate reconciliation, omitted liabilities, unsupported ITC positions or non-compliance discovered during scrutiny can create separate substantive exposure under the CGST Act. A late-fee payment does not regularise an incorrect annual return.
What should finance teams reconcile before filing GSTR-9C?
1. Turnover: reconcile audited financial statements, GSTR-1, GSTR-3B and GSTR-9, including branch and GSTIN-level mapping.
2. Tax liability: identify unreconciled output-tax differences, rate errors, place-of-supply issues and prior-period adjustments.
3. Input tax credit: reconcile books, GSTR-2B, GSTR-3B reversals and year-end adjustments, including blocked-credit and section 16 conditions.
4. Credit/debit notes: confirm that post-year-end notes relating to FY 2025-26 are treated consistently in the annual-return reconciliation.
5. Multi-GSTIN entities: ensure PAN-level audited figures are properly allocated to the GSTIN for which GSTR-9C is being prepared.
6. Additional liability: identify items that need separate payment or disclosure before finalising the reconciliation statement.
The practical filing sequence
A better year-end workflow is: close the books → complete GSTIN-wise turnover and ITC reconciliations → draft GSTR-9 → prepare the GSTR-9C reconciliation in parallel → clear management/auditor review points → file both within the statutory timeline. The objective is to avoid a situation where GSTR-9 is filed simply to meet the date while the reconciliation statement remains incomplete.
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Frequently asked questions
If GSTR-9 is filed on time but GSTR-9C is late, is late fee still payable?
Yes, where GSTR-9C is applicable. CBIC has clarified that the annual return is incomplete until the required GSTR-9C is furnished, so section 47(2) late fee can continue for the delay period.
Is the late fee charged separately for GSTR-9 and GSTR-9C?
No. Circular 246 clarifies that there is one late-fee computation for delay in furnishing the complete annual return, rather than two independent late fees for the two forms.
Can a taxpayer avoid this issue by filing GSTR-9C much later?
Filing later may complete the annual return, but it does not stop the late-fee clock retrospectively. The better approach is to prepare GSTR-9 and GSTR-9C together and resolve reconciliation differences before the due date.
What is the ordinary due date for FY 2025-26?
The ordinary statutory annual-return due date is 31 December 2026, unless the Government subsequently extends it. Taxpayers should verify any later notification before filing.
How PGT & Associates can help
PGT & Associates assists businesses with GST annual-return readiness, GSTR-9/GSTR-9C reconciliation, turnover and ITC diagnostics, mismatch analysis and documentation before filing. For material or multi-GSTIN differences, early reconciliation is generally more useful than a last-week compliance exercise.
Disclaimer
This article is for general professional information and is based on the law and official guidance available as of 24 August 2026. GST due dates, waivers and procedural requirements can be changed by later notifications or portal updates. Obtain advice based on the specific facts and current law before taking a filing or litigation position.
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