GST Audit Limit and GSTR-9C Applicability for FY 2025-26: Who Must File by 31 December 2026

24 Oct 2026

Updated 3 November 2026 · By Regi Tom Antony, FCA, MBA (Australia), ACMA (UK), CGMA (USA), CISA (USA), Managing Partner, Regi Tom Antony & Associates, Chartered Accountants, Kochi (est. 1997). Former Group CFO/COO (OSRAM/Siemens, Westcon Group; Middle East & Africa) and author of NRI Tax Blueprint.

Many businesses still ask for a "GST audit" when their turnover crosses ₹2 crore or ₹5 crore. The CA-certified GST audit under section 35(5) of the CGST Act ended on 1 August 2021. What applies today is a two-step test: whether you must file the annual return (GSTR-9), and whether you must also file the reconciliation statement (GSTR-9C). This guide sets out both for FY 2025-26, the year now being closed, with the 31 December 2026 deadline.

GSTR-9 and GSTR-9C applicability at a glance (FY 2025-26)

Is there still a GST audit by a Chartered Accountant?

Not as a statutory requirement. The Finance Act, 2021 omitted section 35(5) of the CGST Act from 1 August 2021, and Rule 80(3) was amended so that GSTR-9C is self-certified. Two other kinds of GST audit still exist, and both are initiated by the department rather than the taxpayer:

• Departmental audit (section 65): conducted by GST officers on notice, usually at your premises.
• Special audit (section 66): ordered by the Commissioner where the value or ITC claimed appears incorrect, and carried out by a CA or CMA nominated by the department.

In practice, a Chartered Accountant still prepares most GSTR-9C statements, because the form reconciles turnover, tax and input tax credit in the audited financial statements with the returns filed during the year.

How to compute aggregate turnover for the ₹2 crore and ₹5 crore limits

Aggregate turnover under section 2(6) of the CGST Act is computed on an all-India PAN basis, not GSTIN by GSTIN. Add taxable supplies, exempt supplies, exports and inter-state supplies across every registration on the same PAN. Leave out GST itself and inward supplies taxed under reverse charge. A business with three State registrations of ₹2 crore each has aggregate turnover of ₹6 crore, so every one of those GSTINs files GSTR-9C.

What changed for FY 2025-26

• GSTN enabled the GSTR-9 and GSTR-9C tiles for FY 2025-26 on 8 October 2026. All GSTR-1 and GSTR-3B returns for the year must be filed first.
• A CBIC notification dated 26 October 2026, effective 1 November 2026, carries the GSTR-9 table relaxations into FY 2025-26 onwards. Exempt and nil-rated supplies may be combined in Table 5D. Inputs and input services may be combined in Tables 6B to 6D, with capital goods shown separately. Tables 15, 16 and 18 are optional. Table 17 (HSN summary of outward supplies) remains mandatory, subject to the instructions.
• The ₹2 crore GSTR-9 exemption under Notification No. 15/2025-Central Tax continues to apply.

Due date and late fee

Both GSTR-9 and GSTR-9C for FY 2025-26 are due on 31 December 2026. Late fees under section 47(2), as rationalised by Notification No. 07/2023-Central Tax, are:

GSTR-9C preparation checklist

1. Reconcile turnover in the audited financial statements with GSTR-9: unbilled revenue, advances, credit notes issued after year-end and branch transfers are the usual differences.
2. Reconcile ITC in the books with GSTR-2B and GSTR-3B, and confirm that blocked credits under section 17(5) and reversals under Rule 42 and 43 are reflected.
3. Claim any missed FY 2025-26 ITC through GSTR-3B by 30 November 2026; it cannot be claimed in GSTR-9.
4. Pay any additional tax identified through Form DRC-03 before filing, with interest under section 50.
5. Keep a working file explaining every unreconciled difference. It is the first document an officer asks for in a section 65 audit.

Frequently asked questions

What is the GST audit limit for FY 2025-26?

There is no longer a CA-certified GST audit. What remains is the GSTR-9C reconciliation statement, required when aggregate turnover for FY 2025-26 exceeds ₹5 crore. GSTR-9C is self-certified by the taxpayer and is due with GSTR-9 by 31 December 2026.

Is GSTR-9 mandatory for turnover below ₹2 crore?

No. Under Notification No. 15/2025-Central Tax dated 17 September 2025, registered persons with aggregate turnover up to ₹2 crore are exempt from filing GSTR-9 from FY 2024-25 onwards. They may still file it voluntarily.

Does GSTR-9C need a CA or CMA certificate?

No. Since 1 August 2021, when section 35(5) of the CGST Act was omitted and Rule 80(3) amended, GSTR-9C is self-certified by the taxpayer. A CA or CMA usually still prepares it, because it reconciles the audited financial statements with the GST returns.

How is aggregate turnover calculated for the ₹2 crore and ₹5 crore limits?

Under section 2(6) of the CGST Act, aggregate turnover is computed on an all-India PAN basis. It includes taxable, exempt, export and inter-state supplies across all GSTINs on the same PAN, and excludes GST itself and inward supplies taxed under reverse charge.

What is the late fee for filing GSTR-9 after 31 December 2026?

Under Notification No. 07/2023-Central Tax, the late fee is ₹50 a day (CGST and SGST together) capped at 0.04% of turnover in the State for turnover up to ₹5 crore, and ₹100 a day capped at 0.04% for turnover above ₹5 crore up to ₹20 crore. Above ₹20 crore it is ₹200 a day, capped at 0.5% of turnover in the State, under section 47(2).

Can I still claim missed ITC for FY 2025-26 in GSTR-9?

No. GSTR-9 only reports ITC already claimed. Missed ITC for FY 2025-26 must be claimed in a GSTR-3B filed by 30 November 2026 (or by the date the annual return is filed, if earlier) under section 16(4) of the CGST Act. Any extra tax found while preparing GSTR-9 or 9C is paid through Form DRC-03.

Related guides

• GST return due dates for FY 2026-27
• GST compliance and audit services in Kochi
• GST refund: RFD-01 process and time limit
• Income tax audit limit u/s 44AB (AY 2026-27)
• Corporate tax and compliance deadline calendar

Sources

• CGST Act, 2017 — sections 2(6), 16(4), 35, 44, 47, 50, 65 and 66; CGST Rules, 2017 — Rule 80 (cbic-gst.gov.in)
• Notification No. 15/2025-Central Tax dated 17 September 2025; Notification No. 07/2023-Central Tax dated 31 March 2023; CBIC notification dated 26 October 2026
• GSTN advisory on GSTR-9/9C for FY 2025-26 (gst.gov.in)

Regi Tom Antony & Associates prepares GSTR-9 and GSTR-9C reconciliations for businesses across Kerala and India. If your aggregate turnover crossed ₹5 crore in FY 2025-26, or you are unsure how multiple GSTINs add up, contact our GST team well before 31 December 2026.

This article is for general information and reflects the position as at 3 November 2026. Check the latest CBIC notifications before filing.