GSTR-9C Applicability for FY 2025-26: ₹5 Crore Threshold, Self-Certification & Due Date

For FY 2025-26, GSTR-9C is required where a registered person’s aggregate turnover during the financial year exceeds ₹5 crore. The statement is self-certified and is furnished with Form GSTR-9. Under the current Rule 80(3) framework, the normal due date is 31 December following the end of the financial year; for FY 2025-26, that means 31 December 2026 unless the Government extends the deadline.

Who must file GSTR-9C for FY 2025-26?

Rule 80(3) of the CGST Rules applies where aggregate turnover during the financial year exceeds ₹5 crore. CBIC’s Circular No. 246/03/2025-GST, dated 30 January 2025, expressly records the post-1 August 2021 position: taxpayers crossing the ₹5 crore threshold furnish a self-certified reconciliation statement in Form GSTR-9C along with Form GSTR-9.

The word “exceeds” matters. A taxpayer whose aggregate turnover is exactly ₹5 crore does not cross the Rule 80(3) threshold merely by reaching ₹5 crore. Once turnover goes above ₹5 crore, the GSTR-9C requirement should be evaluated.

How is the ₹5 crore threshold tested?

The CGST Act defines aggregate turnover on an all-India basis for persons having the same PAN. It includes taxable supplies, exempt supplies, exports and inter-State supplies, while excluding GST and cess and excluding inward supplies on which tax is payable under reverse charge.

This makes the threshold test especially important for groups operating through multiple GST registrations. Finance teams should not test the ₹5 crore threshold by looking at one branch ledger in isolation. The PAN-level aggregate turnover position should be established first, and the annual-return workflow should then be completed for the relevant GST registrations.

Is GSTR-9C still required to be certified by a CA or CMA?

No separate GST audit certification by a chartered accountant or cost accountant is mandated under the post-1 August 2021 framework. Section 44 now refers to a self-certified reconciliation statement, and Rule 80(3) requires Form GSTR-9C to be self-certified. This is different from the pre-1 August 2021 regime, when the reconciliation statement was linked to the statutory GST audit requirement.

That does not make the exercise informal. GSTR-9C still reconciles the annual GST reporting with the audited annual financial statements. A company may also have separate audit requirements under the Companies Act, Income-tax Act or other applicable law. The GST filing responsibility and the quality of the reconciliation therefore remain significant even though the GSTR-9C itself is self-certified.

What should be reconciled before filing GSTR-9C?

A strong GSTR-9C process should start well before the annual-return deadline. The objective is not simply to make portal totals agree; it is to explain why the audited financial statements, GST returns and tax positions differ and to preserve evidence for those differences.

• Turnover in audited financial statements versus turnover reported through GSTR-1, GSTR-3B and the annual return.

• Credit notes, debit notes, amendments, advances, exports, exempt or non-GST supplies and year-end cut-off items.

• Tax payable versus tax actually discharged, including reverse-charge and other adjustments where relevant.

• Input tax credit recorded in the books versus GST return data, with unresolved supplier-side or GSTR-2B differences separately tracked.

• State-wise or GSTIN-wise allocation issues for entities operating through multiple registrations.

• Prior-period corrections and voluntary payments, with a clear audit trail for the reason and period to which each adjustment relates.

Why filing GSTR-9 alone may not complete the annual return

CBIC Circular No. 246/03/2025-GST gives this point unusual importance. Where GSTR-9C is required, CBIC has clarified that the annual return under Section 44 is not complete merely because GSTR-9 has been filed. The annual return is treated as complete only when both GSTR-9 and the required GSTR-9C have been furnished.

The same circular clarifies the late-fee consequence. Late fee under Section 47(2) is calculated for the delay in furnishing the complete annual return, from the due date until the required GSTR-9 and GSTR-9C are both furnished. CBIC also clarifies that separate late fees are not imposed independently for GSTR-9 and GSTR-9C; the relevant period runs until the complete annual-return package is filed.

FY 2025-26 deadline: 31 December 2026

Under Rule 80(3), the reconciliation statement is furnished with the annual return on or before 31 December following the end of the financial year. Accordingly, the normal due date for FY 2025-26 is 31 December 2026. Businesses should still check for any later notification extending the due date before filing.

Waiting until December creates avoidable risk. Annual reconciliation often exposes timing differences, missing supplier documents, classification issues and tax-payment differences that need investigation before management can self-certify the statement.

A practical GSTR-9C preparation sequence

• Confirm PAN-level aggregate turnover and document why GSTR-9C is or is not applicable.

• Freeze the audited financial-statement numbers and map them to each GST registration.

• Reconcile outward supplies across books, GSTR-1, GSTR-3B and GSTR-9 before preparing GSTR-9C.

• Reconcile ITC and isolate GSTR-2B or supplier-reporting exceptions rather than netting them away.

• Quantify unexplained tax differences and decide the appropriate corrective or payment action before certification.

• Maintain a reconciliation file containing workings, explanations, supporting documents, management sign-off and filing acknowledgements.

How GSTR-9C fits with the other FY 2025-26 GST work

If your immediate concern is the annual return itself, see our GSTR-9 late filing, turnover caps and annual-return compliance guide. GSTR-9C should be treated as part of the same year-end reconciliation process where the ₹5 crore threshold is crossed.

For input-tax-credit exceptions identified during the annual reconciliation, our GSTR-2B mismatch guide for FY 2025-26 explains the supplier-reconciliation workflow and the time-sensitive risks around unresolved invoices.

You should also review the 30 November 2026 ITC time-limit guide under Section 16(4) before treating year-end ITC differences as matters that can simply be corrected when GSTR-9C is prepared.

Frequently asked questions

Is GSTR-9C applicable if turnover is exactly ₹5 crore?

Rule 80(3) uses the expression “exceeding five crore rupees.” On that wording, exactly ₹5 crore does not cross the GSTR-9C threshold.

Is GSTR-9C a CA-certified GST audit report?

No. Under the current framework, GSTR-9C is a self-certified reconciliation statement. The earlier GST audit certification structure was removed from 1 August 2021.

Can I file GSTR-9 first and GSTR-9C later?

Where GSTR-9C is required, CBIC has clarified that the Section 44 annual return is not complete until both forms are furnished. Filing GSTR-9 first therefore does not eliminate the exposure created by a delayed required GSTR-9C.

What is the normal due date for FY 2025-26?

The normal statutory date is 31 December 2026, subject to any extension that may subsequently be notified.

Does a multi-state business test the ₹5 crore threshold separately for each GSTIN?

The statutory concept of aggregate turnover is PAN-based and computed on an all-India basis. Multi-state businesses should therefore establish the PAN-level turnover position before completing GSTIN-level annual-return and reconciliation work.

Primary sources

The key current position is set out in CBIC Circular No. 246/03/2025-GST dated 30 January 2025, including the ₹5 crore threshold, self-certification, 31 December timeline and late-fee clarification. CBIC’s official aggregate-turnover FAQ explains the PAN-based all-India definition used under Section 2(6) of the CGST Act.

Professional assistance

PGT & Associates can assist businesses with FY 2025-26 GSTR-9 and GSTR-9C applicability testing, PAN-level turnover analysis, books-to-GST reconciliation, ITC exception review, documentation of adjustments and annual-return filing support. The objective should be a defensible reconciliation file, not merely a portal submission.

Disclaimer

This article is for general professional information and does not constitute legal, tax or accounting advice. GST provisions, notifications, portal functionality and due dates may change. Taxpayers should verify the law and facts applicable to their specific case before taking action.