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Published on: Jun 24, 2026

GST Audit & Certifications - By Chartered Accountants

GST audit would have to be periodically conducted on entities registered under GST by a

Practising Chartered Accountant or GST officer to ensure that proper compliance is maintained. In this article, we look at the different types of GST audit and certifications conducted or provided by a practising Chartered Accountant from time to time.

GST Annual Return

All entities required to file monthly

GST returns are required to file GST annual return before 31st December of each financial year. Only Input Service Distributors, Casual Taxable Persons and Non-Resident Taxable persons are exempt from filing GST annual return. Entities required to file GST annual return having an aggregate turnover of over Rs.2 crores in a financial year must get the annual GST accounts audited and certified by a practising Chartered Accountant. Know more about GST Return Due Dates.

GST Input Tax Credit Claim under Special Circumstances

For instance, a registered person files FORM GST ITC-01 within 30 days of becoming eligible to avail input tax credit on existing stocks. In the details furnished in the declaration for the claim of input tax credit under special circumstances, Chartered Accountant certification shall apply if the aggregate value of the claim on account of central tax, State tax, Union territory tax and integrated tax exceeds Rs.2 lakhs. In an input tax credit claim under special circumstances, where the tax invoices related to the inputs held in stock are not available, the registered person can estimate the amount based on the prevailing market price of the goods on the effective date. In these instances, a practising chartered accountant or cost accountant shall duly certify the details provided by the taxpayer. Know more about

input tax credit under GST.

Special Audit Ordered by GST Officer

A GST Officer (not below the rank of Assistant Commissioner) can order for scrutiny, inquiry or investigation if at any stage of scrutiny, inquiry, investigation or any other proceedings believes that the entity failed to declare the correct value or the credit availed mismatches within the normal limits. In such cases, the GST Officer with the prior approval from the Commissioner shall direct the taxpayer to provide the records including books of account examined and audited by a Chartered Accountant or Cost Accountant. After issuing the directions for special audit through FORM GST ADT-03 to the registered person, the nominated Chartered Accountant should submit the audit report duly signed and certified by the CA to the Assistant Commissioner within a period of 90 days. In case of difficulty in completing the audit within the provided time period, the registered person or the chartered accountant for any material and sufficient reason, request for an extension of the period by an additional 90 days.

Sample Special Audit Order Sample Special Audit Order Simplify your GST registration and GST return filing process with IndiaFilings experts!
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Frequently Asked Questions

Common questions about GST Audit & Certifications by Chartered Accountants in India.

A GST audit is a periodic examination conducted by a practicing Chartered Accountant or GST officer to ensure that an entity registered under GST is maintaining proper compliance with the relevant laws and regulations. The audit aims to verify the accuracy and completeness of the entity's GST returns, records, and transactions.
Entities registered under GST with an aggregate turnover exceeding Rs. 2 crores in a financial year are required to get their annual GST accounts audited and certified by a practicing Chartered Accountant. Additionally, a GST officer can order a special audit if they suspect any non-compliance or irregularities.
When a registered person files FORM GST ITC-01 to claim input tax credit on existing stocks under special circumstances, and the aggregate value of the claim exceeds Rs. 2 lakhs, a Chartered Accountant's certification is required. This certification ensures the accuracy and validity of the details provided in the declaration.
A GST officer, not below the rank of Assistant Commissioner, can order a special audit with prior approval from the Commissioner if they believe that the entity has failed to declare the correct value or the input tax credit availed is mismatched. In such cases, the entity must provide records, including books of account, examined and audited by a Chartered Accountant or Cost Accountant.
After receiving the directions for a special audit through FORM GST ADT-03, the nominated Chartered Accountant must submit the audit report, duly signed and certified, to the Assistant Commissioner within 90 days. However, an extension of an additional 90 days can be requested if there are material and sufficient reasons for the delay.
All entities required to file monthly GST returns must file a GST annual return before December 31st of each financial year. However, Input Service Distributors, Casual Taxable Persons, and Non-Resident Taxable Persons are exempt from filing the GST annual return.
Entities required to file a GST annual return and having an aggregate turnover exceeding Rs. 2 crores in a financial year must get their annual GST accounts audited and certified by a practicing Chartered Accountant.
The primary purpose of a Chartered Accountant's certification in a GST audit is to provide an independent and professional assessment of the entity's compliance with GST laws and regulations. This certification enhances the credibility and accuracy of the entity's GST records and returns.
Yes, if there are material and sufficient reasons, the registered person or the Chartered Accountant can request an extension of up to an additional 90 days for submitting the special audit report.
Failure to comply with GST audit requirements, such as not getting the annual GST accounts audited or not providing records for a special audit, can result in penalties and legal consequences under the GST laws. It is essential for entities to maintain proper compliance and cooperate with the audit processes to avoid any potential issues.