Preparing for a GST Department Audit: Key Steps and Focus Areas

GST

Preparing for a GST Department Audit: Key Steps and Focus Areas

GST

Receiving a GST audit notice from the department can be an intimidating experience for any business. However, with timely preparation and a systematic approach, it is possible to handle the audit process efficiently and avoid penalties. This guide outlines the essential steps to take upon receiving a GST audit notice, key reconciliation tasks, common audit focus areas, and best practices to ensure compliance.

1. Understand the Audit Notice

The first and most crucial step is to thoroughly review the audit notice. It typically contains vital information such as the scope of the audit, audit period, the legal provision under which it is initiated (usually Section 65 or 66 of the CGST Act), and the details of the audit officer. Businesses should also take note of any deadlines for document submission or meetings.

2. Verify GST Returns and Conduct Reconciliations

Before the audit begins, businesses must ensure that all GST returns—GSTR-1, GSTR-3B, GSTR-9, and GSTR-9C (if applicable)—are filed and reconciled with their financial records. Key reconciliation areas include:

  • Sales and purchase ledgers vs. GST returns

  • Input Tax Credit (ITC) claimed vs. GSTR-2B

  • Output tax liability vs. sales registers

  • E-invoice and E-way bill data vs. GSTR-1 and sales registers

Maintaining an accurate stock register and general ledger is also essential, as discrepancies here are common triggers for scrutiny.

GST

3. Organize Required Documents

Proper documentation is critical during a GST audit. Businesses should organize and keep ready the following:

  • GST registration certificate

  • All filed GST returns (monthly and annual)

  • Tax invoices and e-way bills

  • Purchase and sales registers

  • Input and output tax ledgers

  • Stock and expense registers

  • Trial balance, profit & loss statement, and balance sheet

  • Bank statements

  • All reconciliation workings and justifications for past entries

Digital organization of these files by GSTIN, financial year, and document type can significantly ease the audit process.

4. Key Areas of Focus for GST Auditors

Audit officers often focus on common areas of non-compliance. Businesses should proactively verify:

  • Excess ITC claimed or mismatch with GSTR-2B

  • Non-payment to suppliers within 180 days and reversal of ITC, if applicable

  • Undisclosed or under-reported outward supplies

  • Valuation discrepancies or under-valuation of supplies

  • Reverse Charge Mechanism (RCM) compliance

  • Tax liability on advances and time of supply

  • Transactions with related parties

  • Apportionment of ITC between taxable, exempt, and non-GST supplies

5. Specific Compliance Checks That Attract Penalties

Even in the absence of major discrepancies, auditors frequently verify smaller compliance points that carry direct penalties. Businesses should review:

  • Filing of ITC-04 for goods sent to job workers

  • Declaration of all bank accounts linked to the business in the GST portal (failure to declare can attract a penalty of ₹25,000 per undeclared account)

  • HSN code reporting: Ensure the top five HSNs are updated and match invoices and returns

  • GSTR-1 summaries: Ensure document summaries and HSN tables are correctly filed

  • Updated business addresses: Any change in the principal or additional place of business must be updated within 30 days

  • E-invoice and e-way bill data: Must match GSTR-1; any mismatch can lead to per-invoice penalties

6. Voluntary Correction and DRC-03

If any past errors or shortfalls are discovered during pre-audit checks, businesses can voluntarily pay the differential tax using Form DRC-03. This proactive step is often viewed positively and may help in mitigating penalties or interest.

7. Representation and Legal Awareness

While a business owner may choose to appear before the officer, it is advisable to nominate a knowledgeable person such as the accounts head or GST consultant for representation. All submissions must be in written form and duly acknowledged by the officer.

It also helps to be familiar with the key legal provisions related to audits:

  • Section 65 – Departmental Audit

  • Section 66 – Special Audit by Chartered Accountant or Cost Accountant

  • Section 70 – Power to summon documents or persons

  • Rule 101 – Procedure of audit

GST

8. Importance of Professional Assistance

Engaging a Chartered Accountant or GST expert can prove invaluable. They can conduct a pre-audit review, simulate likely questions, and help in preparing reconciliations and documentation. Their support ensures that the business is well-prepared and compliant, significantly reducing audit risks.

Read More: Claiming Delayed Income Tax Refunds: Relief Through CBDT’s Special Provisions

A GST audit is not just a compliance exercise—it is a test of the accuracy, transparency, and discipline of your tax practices. Being proactive, meticulous, and professionally guided can ensure a smooth audit experience and protect your business from unnecessary financial and legal exposure.

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Understanding Form 3CD Amendments: What Changed from April 1, 2025

Form 3CD

Understanding Form 3CD Amendments: What Changed from April 1, 2025

Form 3CD

The Central Board of Direct Taxes (CBDT), via Notification No. 23/2025 dated March 28, 2025, has introduced key amendments to Form 3CD under the Income-tax Rules, 1962. These changes come into effect for all tax audit reports signed on or after April 1, 2025, and are applicable for Assessment Year 2025–26 onwards.

Key Amendments and Practical Implications

1. Clause 12 – Presumptive Income under Section 44BBC

A new clause has been added to cover entities engaged in broadcasting and production opting for presumptive taxation. Tax professionals should proactively identify clients who may fall under this category to ensure timely and correct reporting.

Form 3CD

2. Clause 19 – Chapter VI-A Deductions

Deductions under Sections 80-IB, 80-IC, and 80-ID have been removed. These sections have lost relevance, and their omission aligns the reporting format with current tax law.

3. Clause 21 – Disallowance under Section 43B

A new reporting requirement has been introduced for “Settlement Expenses” under disallowances. This becomes relevant in cases involving contractual dispute settlements or negotiated resolutions. Teams should closely examine expense classifications during audits.

4. Clause 22 – Interest Payable under MSMED Act

Auditors are now required to report interest payable to Micro and Small Enterprises, regardless of whether the interest has been paid. This change demands accurate vendor classification and a reliable ageing analysis of outstanding dues.

5. Clause 23 – Buy-back of Shares under Section 115QA

This clause now requires disclosure of the amount received and the acquisition cost of shares in buy-back transactions. Auditors must scrutinise valuation methodology and ensure all supporting documents are in place.

6. Clause 26 – TDS on Payments to Non-Residents

This clause has been expanded to include more detailed reporting on TDS compliance related to payments made to non-residents. With increased scrutiny of foreign remittances, maintaining detailed documentation is now more critical than ever.

7. Clauses 28 and 29 – Reporting under Sections 56(2)(viia) and 56(2)(viib)

These clauses have been removed due to legislative changes, simplifying reporting in this area.

8. Clause 31 – Reporting of Loans and Deposits

The clause now requires mandatory classification of loans and deposits into twelve specific categories. This change allows tax authorities better visibility and tracking. Practitioners must ensure all entries are reconciled with the books of accounts and categorised appropriately.

9. Clause 36B – Newly Inserted for Buy-back Transactions

A new clause, Clause 36B, has been introduced for additional reporting of buy-back activities under Section 115QA. While somewhat similar to Clause 23, this addition will likely support more refined data analysis by tax authorities.

Effective Date

All amendments are applicable to audit reports signed on or after April 1, 2025, aligning with AY 2025–26.

What This Means for Audit Teams

These changes go beyond compliance—they reflect a broader shift in the way tax audits are expected to function. To stay ahead, firms should:

  • Update internal audit checklists and templates

  • Review client classification procedures, especially for MSME vendors

  • Enhance documentation standards for foreign transactions

  • Educate teams on new clause-level expectations

  • Establish robust reconciliation processes for loans, deposits, and buy-back entries

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Deadline for Income Tax Audit Report Extended to October 7, 2024

Deadline for Income Tax Audit Report Extended to October 7, 2024

The Income Tax Department has announced an extension for the submission of the income tax audit report for the financial year 2023-24. Taxpayers who were initially required to submit their audit reports by September 30, 2024, can now do so by October 7, 2024. This extension allows additional time for those mandated by law to conduct an income tax audit and file the corresponding report online via the Income Tax e-filing portal.

Significance of the Extension

This extension is crucial as late submission of the tax audit report can result in significant penalties. Taxpayers who miss the deadline could face a fine of either ₹1.5 lakh or 0.5% of their total sales, whichever is lower. Therefore, the new deadline offers some relief for businesses and individuals who need more time to complete their audit obligations.

Official Announcement from the CBDT

The Central Board of Direct Taxes (CBDT) made the announcement on September 29, 2024, through a circular. The circular states:

CBDT has decided to extend the specified date for filing various audit reports for the financial year 2023-24, which was originally set for September 30, 2024, for assessees referred to in clause (a) of Explanation 2 to sub-section (1) of section 139 of the Income Tax Act. The deadline is now extended to October 7, 2024.

Who Benefits from the Extension?

According to the circular, this extension applies to all taxpayers required to undergo a tax audit. This includes individuals, companies, and other entities whose Income Tax Returns (ITRs) are due by October 31, 2024. Anyone who was originally required to submit their tax audit report by September 30 can now take advantage of the extended deadline and file by October 7, 2024.

For taxpayers who fall under the mandatory audit category, this extension offers crucial extra time to ensure compliance without incurring penalties. Make sure to upload your tax audit report by the new deadline to avoid any late fees or penalties.

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