GST annual return, GSTR-9C reconciliation and GST audit support

Under the CGST Act, an audit under Section 65 is conducted by the Commissioner or an officer authorised by him, after notice in Form GST ADT-01. A special audit under Section 66 is directed by the department and done by a CA/CMA it nominates. Separately, taxpayers above ₹5 crore aggregate turnover file a self-certified reconciliation (GSTR-9C) with the annual return. People often call any of these a 'GST audit'.

A Section 65 audit is conducted by the tax officer. A Section 66 special audit is done by a Chartered Accountant or Cost Accountant nominated by the Commissioner. GSTR-9C is now self-certified by the taxpayer; a CA can prepare and review it for you.

No CA audit is mandated by turnover. From FY 2020-21 onwards (s.35(5) omitted and rule 80(3) amended w.e.f. 1 Aug 2021), taxpayers above ₹5 crore file a self-certified GSTR-9C. For FY 2017-18 to 2019-20 a CA/CMA-certified reconciliation applied (above ₹2 crore; ₹5 crore for FY 2018-19 and 2019-20). Ask us about older periods.

The annual return (GSTR-9) and, where applicable, the self-certified GSTR-9C are due by 31 December following the end of the financial year, subject to any extension notified by the government.

You need GSTR-1, GSTR-3B, GSTR-2A/2B, purchase and sales registers, e-way bills, e-invoices, input tax credit records, audited financial statements, and supporting invoices for the financial year.

Form GST ADT-01 is the notice by which a tax officer tells you that an audit under Section 65 will be conducted. It is not a report you or your CA file. The findings of that audit are communicated in Form GST ADT-02.

CBIC Circular 246/03/2025-GST explains how the late fee under Section 47 applies when GSTR-9C is furnished after the annual return. The amount depends on the period and the notifications in force, so we check it for your case.

Yes, but a late fee under Section 47 can apply. We recommend filing on time and checking any notified extension or late-fee waiver for your year.

An audit under Section 65 examines your records and returns after notice in ADT-01. An inspection, search or seizure under Section 67 is an enforcement power used where the officer has reasons to believe there is evasion. Both are carried out by the department, not by a taxpayer-appointed CA.

No. There is no turnover-based audit from FY 2020-21 onwards. Taxpayers above ₹5 crore file a self-certified GSTR-9C; any registered person may receive a departmental audit notice.

Yes. Your statutory auditor or another CA can prepare and review GSTR-9C, which is now self-certified by the taxpayer.

Common findings include ITC claimed on ineligible supplies, mismatched GSTR-2A/2B and GSTR-3B ITC, incorrect place of supply, wrong GST rates, missing invoices, and non-reversal of ITC on exempt supplies.

GSTR-9 annual return filing starts from ₹2,499 plus GST. GSTR-9C preparation and departmental or special audit support are quoted after we see your turnover, number of GSTINs and records.

Reconciling your returns, ITC and books before GSTR-9/9C lets you correct discrepancies yourself, before the department identifies them in an audit or scrutiny.

Read the notice for the period, the documents requested and the date. Organise your returns, books and ITC records, and reply within the time given. We can prepare the records and replies and attend to the officer's queries with you.