25 June 2025

GST Audit Under Section 65 of GST Law : Everything You Need to Know as a Finance Leader

The Goods and Services Tax (GST) law in India emphasizes compliance and transparency in tax administration. A critical mechanism to uphold these principles is the audit process. Section 65 of the GST Act outlines the framework for audits conducted by tax authorities to scrutinize a taxpayer’s financial records, returns, and statements, ensuring adherence to tax regulations. Understanding this provision is vital for businesses to maintain compliance, avoid penalties, and assess their GST obligations effectively.

What is an Audit Under Section 65 of GST? Under Section 65 of the Central Goods and Services Tax (CGST) Act, 2017, the Commissioner or an authorized officer has the authority to conduct audits of any registered taxpayer to ensure proper tax compliance. This audit involves a thorough examination of the taxpayer's financial records, GST returns, and other pertinent documents.

Primary Objectives of the Audit The main goals of the audit are to: 

• Verify the accuracy of declared tax liabilities.  • Ensure compliance with GST provisions. • Identify any instances of tax evasion or irregularities.

๐Ÿงพ Key Legal Features: Initiation and Conduct of Audits •

๐Ÿ“Location: The audit may be carried out either at the taxpayer’s place of business or in the tax office.

๐Ÿ“… Prior Notice: A notice must be issued at least 15 days before the commencement of audit.

๐Ÿ•’ Timelines: The audit must be completed within 3 months from the commencement date, extendable up to 6 months by the Commissioner in justified cases [Section 65(4)].

๐Ÿ“œ Procedural Framework: Governed under Rule 101 of the CGST Rules, outlining officer responsibilities, timelines, and documentation

Key Aspects of a GST Audit Under Section 65

1. Scope of Audit: The audit encompasses all financial records, tax invoices, books of accounts, and returns filed by the taxpayer.

2. ๐Ÿ‘จ๐Ÿ’ผ Authority of the Officer: The officer conducting the audit has the authority to seek explanations, examine documents, and verify tax payments.

3. ๐Ÿ“ข Timeline: The audit must be completed within three months from the start date, with a possible extension of six months in special circumstances.

4. ๐Ÿ“ Final Findings: After the audit, the tax officer will communicate the findings to the taxpayer, highlighting any discrepancies identified. If discrepancies are found, taxpayers may receive Form DRC-01A before any adjudication proceedings under Sections 73 or 74

๐Ÿ’ก Key Areas of Focus During a GST Audit Under Section 65

Based on practical experience, audit teams typically concentrate on the following aspects to assess GST liabilities:

1. ๐Ÿ“ฅ Reverse Charge Mechanism (RCM) under Section 9(3) of the CGST Act, 2017: Verification of RCM applicability and compliance concerning services such as security services and advocate fees, often referencing specific ledger accounts within audited financial statements.

2. ๐Ÿšซ Input Tax Credit (ITC) Availed in Excess: Rigorous verification of ITC claims against eligible purchases to prevent the undue utilization of tax credits.

3. ๐Ÿšซ  Ineligible ITC Claims under Section 17(5): Ensuring strict adherence to ITC eligibility criteria, with particular attention to ineligible credits claimed on items like employee insurance, travel expenses, and canteen services.

4.   Penalties for Late Filing under Section 47(1) of the CGST Act, 2017: Review of penalties levied for delays in filing GST-1, GSTR-3B, and GSTR-9 returns.

5. ๐Ÿš— Tax Implications on the Sale of Vehicles under Section 18(6): Confirmation of the appropriate tax treatment applied to the sale of vehicles.

6. ๐Ÿ“ˆ Analysis of Accounts Payable Aging: Examination of the annual AP aging report to identify instances of vendor bills remaining unpaid for periods exceeding 80 days.

7. ๐Ÿ’ธ  Treatment of Bad Debts: Evaluation of the accounting and GST implications of bad debts written off in the financial records.

8. ๐Ÿ“‰  Reconciliation of Turnover: Comparing the declared turnover in income tax returns with the corresponding GST turnover to identify any potential instances of undeclared income, including revenue from scrap sales and other miscellaneous sources.

9. ๐Ÿ”  Verification of Tax Payments and Refund Claims: Reviewing the accuracy of tax amounts paid against the declared turnover and the legitimacy of any refunds claimed during the audit period.

10. ๐Ÿงพ  Applicability of E-Invoicing under Rule 48(4) of the CGST Rules, 2017: Assessing compliance with e-invoicing regulations based on applicable turnover thresholds.

11. ๐Ÿ“˜ Reconciliation with audited financial statements is a key part of GST compliance. It involves verifying:

  • GST treatment of related party transactions
  • Whether depreciation is calculated on gross or net invoice value
  • GST impact of customer advances and prepaid expenses
  • Alignment of year-end GST payables and GST credit ledger balances with GST returns

Accurate Reporting in GST Returns :Ensuring accurate and consistent reporting across GSTR-1, GSTR-3B, and GSTR-9 is crucial. This includes:

  • Timely ITC and RCM reversals
  • Correct declaration of taxable turnover
  • Rectification of clerical errors or excess claims
  • Matching returns with books to prevent mismatches

Accurate reporting builds a strong compliance record and reduces audit risk.

12. ๐Ÿ“œ Review of Prior Tax Deposits for Appeals: Identifying any pre-deposits made in relation to service tax or GST appeals to gain insights into past notices and their underlying reasons.

13. ๐Ÿ” Extended Scope of Examination: While the aforementioned areas represent primary focus points, audit teams may extend their scrutiny based on their professional judgment and the specific documentation provided by the taxpayer, potentially identifying additional aspects of GST liability.

14. Credit & Debit Notes (Sec. 34 – CGST Act): Audit focuses on timely issuance (by 30th Sept of next FY or before annual return), accurate ITC reversal on credit notes, proper linkage of debit notes with original supplies, and correct tax adjustments. Verifies documentation, GST rate consistency, sequential numbering, and use of notes for genuine value adjustments—not for turnover suppression or improper ITC claims.

15. TDS/TCS Non-compliance (Sections 51 & 52) : Issue: Government entities, e-commerce operators may not deduct or deposit TDS/TCS correctly. ๐Ÿงพ Audit Focus: TDS 2% (sec 51) and TCS 1% (sec 52) compliance. ๐Ÿ› ️ Fix: Ensure monthly returns (GSTR-7 / GSTR-8) and tax deposit is made.

Post-Audit Consequences Following the Audit :

No Discrepancies Found: If the audit concludes without identifying any inconsistencies, no further action is required.

⚠️ Discrepancies Identified:  Form DRC-01A may be issued for voluntary compliance before show-cause.

• In cases where discrepancies are noted, the taxpayer will typically be required to rectify the errors and remit any outstanding tax, along with applicable interest under Section 50 and penalties under Section 74, including late fees under Section 47(1) for delayed return filings, typically paid as CGST and SGST from the cash ledger via DRC-3

๐Ÿšจ Further Investigation or Legal Proceedings: Instances of significant tax evasion may lead to more detailed investigations or the initiation of legal proceedings by the authorities.

๐Ÿ›ก Strategies for GST Audit Preparedness To navigate audits efficiently:

๐Ÿ—‚ Maintain Robust Documentation: Ensure accurate and organized records.

๐Ÿ”„Regular Reconciliations: Match books of accounts with GST returns(GSTR-1, GSTR-3B, 2B, GSTR-9).

๐Ÿ“จ Clear Past Notices: Proactively resolve open GST queries and past SCNs.

๐Ÿค Extend Full Cooperation: Provide timely and complete information during the audit.

๐Ÿงญ Conclusion: Proactive Compliance is Key A GST audit under Section 65 is a standard procedural check to verify statutory compliance. Well-prepared businesses with transparent practices and accurate reporting generally undergo audits smoothly. However, for entities with errors or procedural lapses, it is imperative to address findings promptly to mitigate interest and penalty exposures. By understanding the scope, implications, and preparation strategies, taxpayers can engage with audit officers constructively and contribute to a transparent, compliant tax ecosystem. Understanding GST audits and being prepared can help businesses navigate the process smoothly and avoid unnecessary complications. Stay compliant, stay informed.


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       Authorization Letter for GST Audit Representation Letter Format