GST Audit Checklist 2026: Documents & Compliance Requirements

In the context of GST, 'audit' means two different things. First, the annual self-reconciliation through GSTR-9 and GSTR-9C that every registered taxpayer must file. Second, a field audit initiated by GST authorities under Section 65 or Section 66 of the CGST Act, where a tax officer examines your records physically.

This guide covers both — but focuses primarily on the self-audit compliance through GSTR-9 and GSTR-9C, since that is what most businesses face annually. If you are subject to a departmental GST audit, the same document checklist applies, but with stricter timelines and an authorized officer examining your records.

GSTR-9 (Annual Return): Mandatory for all GST-registered taxpayers with turnover above Rs 2 crore. Due December 31 each year for the previous financial year. Summarizes all 12 months of outward supplies, inward supplies, and ITC.

GSTR-9C (Reconciliation Statement): Mandatory only for taxpayers with aggregate turnover above Rs 5 crore. Must be certified by a Chartered Accountant or Cost Accountant. Reconciles GSTR-9 data with audited financial statements.

Preparing for either type of audit requires organized records. Use our GST calculator to verify tax amounts during reconciliation, and use myBillPlease to pull all your invoice data in one export for audit preparation.

GSTR-9 has 19 tables organized into 6 parts. Understanding each part helps you prepare the data correctly and avoid mismatches.

Part I (Tables 1-3): Basic Details
Your GSTIN, legal name, trade name, and the financial year. Auto-populated — no data entry needed.

Part II (Tables 4-5): Outward and Inward Supplies Declared in Regular Returns
Tables 4A-4I: Total outward supplies — taxable, zero-rated, nil-rated, and exempt. This must match the aggregate of all your GSTR-1 filings for the year.
Table 5: Outward supplies on which tax is not payable — exemptions, nil-rated, and non-GST supplies.

Part III (Tables 6-8): ITC Declared in Regular Returns
Table 6: Total ITC claimed across all 12 GSTR-3B returns, broken down by inputs, input services, and capital goods.
Table 7: ITC reversed and ineligible ITC (Section 17(5), Rule 42/43 reversals).
Table 8: ITC comparison — what you claimed vs. what was available in GSTR-2B. This is often where discrepancies surface.

Part IV (Tables 9-14): Declarations from Audited Accounts
This is the core of GSTR-9 — declare your outward supplies and ITC as per your audited books. If your GSTR-1 and GSTR-3B have gaps, errors, or omissions, report the correct figures here and pay any additional tax. This section allows you to correct underpaid taxes without paying a penalty (only interest applies if tax was short-paid).

Part V (Tables 15-16): Particulars of Transactions Relating to Previous FY
Table 15: Credit notes and amendments relating to the previous year but reported in the current year's returns.
Table 16: Supplies/tax declared in the current year but relating to the previous year (transition items).

Part VI (Tables 17-19): HSN Details and Late Fee
Table 17: HSN-wise summary of outward supplies — required for all taxpayers from FY 2025-26 onwards.
Table 18: HSN-wise summary of inward supplies — required for all taxpayers.
Table 19: Late fee payable if GSTR-9 is filed after December 31.

These are the most common issues that surface during GSTR-9 preparation and departmental audits. Address each before your annual return filing:

1. GSTR-1 vs GSTR-3B mismatch: If your total taxable turnover declared in GSTR-1 (output tax return) differs from GSTR-3B (payment return) for any month, it creates a mismatch visible to GST authorities in their analytics. Always reconcile GSTR-1 and GSTR-3B totals monthly. Differences are reported in Table 9 of GSTR-9.

2. Excess ITC claimed vs GSTR-2B: Under the current rules, ITC cannot exceed the amounts in GSTR-2B. If your total ITC claimed in GSTR-3B across 12 months exceeds your GSTR-2B, the excess must be reversed with interest. Table 8 of GSTR-9 shows this comparison automatically.

3. ITC not reversed on ineligible inputs: Common items where ITC is often wrongly claimed and not reversed: company cars, directors' meals, employee canteen food, construction costs, and health insurance premiums. Reverse all blocked credits before filing GSTR-9.

4. Inter-unit transactions not declared: Businesses with multiple GST registrations (different states) must declare inter-branch stock transfers as taxable supplies. Stock transferred to another GSTIN without invoicing is a common audit issue.

5. Advance received — GST not paid: GST is payable on advances received for supply of goods and services, at the time of receipt. If you received advances and paid GST only when the invoice was raised, there is a timing mismatch that needs to be reconciled.

6. Export claims without shipping bill: If you claimed zero-rated export benefits but cannot produce shipping bills matching your GSTR-1 export invoices, the exports may be treated as domestic supplies and full IGST may be demanded.

7. RCM not paid on eligible transactions: Companies that receive services from unregistered vendors or specific notified services (GTA, legal services, security services) must pay GST under reverse charge. Unpaid RCM amounts surface during audit examination of your purchase ledger.

8. HSN code errors: Wrong HSN codes — either incorrect category or digit count — appear in Table 17 of GSTR-9 and can attract penalty of Rs 50 per invoice under Section 125.

9. Turnover underreported: GST on all taxable supplies including advances, free samples above threshold, and related party transactions at market value must be included in turnover. Omissions are a primary focus of department audits.

10. ITC on capital goods not tracked for multi-year reversal: ITC on capital goods (machinery, equipment, vehicles) is claimed in the year of purchase but must be tracked for 5 years. If the capital good is sold, transferred, or destroyed within 5 years, proportional ITC reversal is required under Rule 44.