GST Audit and GSTR-9C — Who Files It, Process, Late Fee (2026)

The old GST audit by a CA or CMA under Section 35(5) was removed with effect from 1 August 2021. What remains is Form GSTR-9C, a self-certified reconciliation statement that a regular taxpayer with aggregate turnover above ₹5 crore files along with the annual return GSTR-9 (Rule 80(3)). In this guide, we cover who files it, the process, the due date and the late fee.

What is GSTR-9C?

GSTR-9C reconciles the figures in the annual return (GSTR-9) with the audited annual financial statements for the same GSTIN. Since 1 August 2021 the taxpayer self-certifies it; a CA or CMA certificate is no longer required, though many businesses still have a professional prepare it.

Who Files GSTR-9C?

• Regular taxpayers whose aggregate turnover for the financial year exceeds ₹5 crore, for each GSTIN under that PAN
• Not composition taxpayers (they file GSTR-4), casual or non-resident taxable persons, ISDs, or TDS / TCS registrants, who do not file GSTR-9 at all
• Turnover is the PAN-level aggregate turnover across India, not the turnover of one GSTIN

What is GSTR-9C?

GSTR-9C is the reconciliation statement between: (a) GSTR-9 (annual return), and (b) audited annual financial statements. It covers turnover, taxable value, tax payable and ITC, with reasons for each difference and any additional liability. Self-certified by the taxpayer.

Key Reconciliations

• Turnover: GSTR-1 + GSTR-3B + books
• Output tax: GSTR-1 + GSTR-3B + books
• Input tax credit: GSTR-2B + GSTR-3B + books + RCM
• Tax paid: GSTR-3B + challan + books
• Closing balance: GST ledger + books
• Stock + inventory: GSTR-1 + books + physical
• Capital goods: ITC claimed + books
• RCM: RCM register + books
• Exempt supplies: GSTR-1 + books
• Inter-state + intra-state: state-wise split

GST Audit Process

Step 1: Books Finalisation

Books are finalised for the FY — P&L, Balance Sheet, Cash Flow, Notes. Audited by statutory auditor (if applicable).

Step 2: GST Data Compilation

Compile GSTR-1, GSTR-3B, GSTR-2B, GSTR-9 for the FY. Reconcile with books.

Step 3: GSTR-9C Preparation

Prepare GSTR-9C with the reconciliations, reasons for differences and any additional tax payable (paid through DRC-03).

Step 4: Self-Certification

The authorised signatory reviews and self-certifies the statement with DSC or EVC.

Step 5: GSTN Filing

GSTR-9C is filed on the GST portal after or with GSTR-9, by 31 December following the end of the financial year.

Timeline

Penalty for Non-Compliance

• Late fee under Section 47(2) (Notification 07/2023-CT): turnover above ₹5 crore and up to ₹20 crore, ₹100 a day (₹50 CGST + ₹50 SGST) capped at 0.04% of turnover in the state; above ₹20 crore, ₹200 a day capped at 0.5%
• CBIC Circular 246/03/2025-GST confirms that a late GSTR-9C attracts this late fee; for years up to FY 2022-23 it was waived where GSTR-9C was filed by 31 March 2025
• General penalty under Section 125: up to ₹25,000
• Additional tax found in the reconciliation: pay with interest under Section 50 (18%), or face proceedings under Section 73 or 74

Cost

Frequently Asked Questions