Tax Services – Legal & Business Consultant

 GST Audit

Introduction to GST Audit

The Goods and Services Tax (GST) regime in India mandates businesses to comply with various audit provisions to ensure transparency, accuracy, and accountability in tax filings. A GST audit is an examination of records, returns, and other documents maintained by a taxpayer to verify the correctness of declared turnover, taxes paid, refund claims, and input tax credit (ITC) availed.
Under GST, audits are conducted to minimize tax evasion, detect discrepancies, and ensure compliance with GST laws. Businesses with an annual turnover exceeding the prescribed threshold must undergo a GST audit. The audit process involves a thorough review of financial statements, invoices, and compliance records to ensure adherence to GST regulations.
In this guide, we will explore the different types of GST audits, their applicability, procedures, and frequently asked questions (FAQs) to help taxpayers understand their obligations under the GST law.

Types of GST Audits

1. Statutory Audit under Section 35(5) – Removed this requirement from. 1st August 2021

Previously, Section 35(5) of the CGST Act mandated that every registered taxpayer with an annual aggregate turnover exceeding ₹2 crore in a financial year must get their accounts audited by a Chartered Accountant (CA) or a Cost Accountant (CMA). The taxpayer was required to submit: 

However, the government removed this requirement from 1st August 2021 as part of GST simplification measures. Now, only a self-certified reconciliation statement (GSTR-9C) is required for taxpayers crossing the ₹5 crore turnover threshold. 

Key Changes after Removal of Section 35(5)
2. Audit by Tax Authorities under Section 65

The GST Commissioner or an authorized officer can conduct an audit under Section 65 of the CGST Act. This is a departmental audit where tax officials examine a taxpayer’s books, records, and returns to verify compliance. 

Applicability & Process
Consequences of Non-Compliance
3. Special Audit under Section 66

Special Audit is ordered under Section 66 when the GST authorities suspect discrepancies in a taxpayer’s records. Unlike a regular audit, this is conducted by a CA/CMA nominated by the Commissioner, even if the taxpayer’s turnover is below the audit threshold. 

When is a Special Audit Initiated?
Procedure for Special Audit
Implications of Special Audit Findings

Frequently Asked Questions (FAQs) on GST Audit

Who is required to undergo a GST audit?
  • Businesses with turnover exceeding ₹5 croremust file GSTR-9C (self-certified).
  • Taxpayers below ₹5 crore are exempt from audit requirements.
  • Invoices (sales & purchases)
  • GST returns (GSTR-1, GSTR-3B, GSTR-9)
  • Bank statements & payment records
  • Annual financial statements 
  • The taxpayer must pay the shortfall with interest (18% p.a.).
  • Penalties may apply if fraud is detected.

Yes, if serious discrepancies are found, the department may initiate a fraud investigation under Section 67.

No, only businesses with ₹5 crore+ turnover must file GSTR-9C.