Who Can Do GST Audit

Who Can Do GST Audit in India? – FAQs

Who can do GST audit in India? The answer depends upon the type of GST audit involved. Under the current GST framework, a departmental audit under Section 65 of the CGST Act is conducted by GST authorities, whereas a Special Audit under Section 66 is conducted by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

The earlier mandatory turnover-based GST audit by a Chartered Accountant or Cost Accountant has been discontinued. Therefore, businesses should distinguish the present GST audit provisions from the earlier GST audit regime.

Businesses requiring professional assistance with departmental audit, GST reconciliation or audit observations can refer to our GST Audit Services in India.

1. Who Can Conduct GST Audit under Section 65?

Under Section 65 of the CGST Act, the Commissioner or an officer authorised by the Commissioner may undertake the audit of a registered person.

The audit may be conducted at:

• the registered person’s place of business; or
• the office of the GST authorities.

Accordingly, a departmental GST audit under Section 65 is conducted by GST authorities and not by a Chartered Accountant independently appointed by the taxpayer.

The authorities may examine GST returns, books of account, input tax credit, turnover, tax payments, refunds and other records to determine compliance with GST law.

For more information about departmental GST audits, read our guide on the Functions of GST Audit Commissionerate.

The statutory provisions can also be referred to on the official CBIC GST website.

2. Who Can Conduct Special Audit under Section 66?

A Special Audit under Section 66 of the CGST Act is conducted by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

A Special Audit may be directed in specified circumstances having regard to factors such as:

• nature and complexity of the case;
• value not being correctly declared;
• credit availed not being within normal limits; and
• interest of revenue.

Therefore, in a Section 66 Special Audit, the registered person does not simply appoint a GST auditor of its own choice.

3. Is GST Audit by a Chartered Accountant Mandatory Based on Turnover?

No.

The earlier provisions requiring specified registered persons crossing the prescribed turnover threshold to have their accounts audited by a Chartered Accountant or Cost Accountant have been discontinued.

Therefore, crossing a particular turnover threshold by itself does not create the earlier mandatory CA/Cost Accountant GST audit requirement.

Businesses should be careful when relying on older GST articles discussing mandatory GST audit based on turnover because they may relate to the earlier law.

4. Can a Chartered Accountant Conduct GST Audit?

It depends upon what is meant by GST audit.

For a departmental audit under Section 65, the audit is undertaken by the Commissioner or an authorised GST officer.

For a Special Audit under Section 66, the audit is conducted by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

Separately, businesses may engage professionals to conduct an internal GST compliance review to identify tax and compliance risks before departmental proceedings arise.

5. Can a Cost Accountant Conduct GST Audit?

A Cost Accountant may conduct a Special Audit under Section 66 when nominated by the Commissioner in accordance with the provisions of the CGST Act.

The same distinction between departmental audit, special audit and voluntary GST compliance review should therefore be maintained.

6. Can a Company Secretary Conduct GST Audit?

A Company Secretary does not conduct the statutory Special Audit contemplated under Section 66, which specifically provides for examination and audit by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

Similarly, a departmental audit under Section 65 is conducted by GST authorities.

This is different from other GST compliance or advisory services that professionals may provide depending upon their scope of practice.

7. Can the Statutory Auditor of a Company Conduct GST Audit?

This question was particularly relevant under the earlier turnover-based GST audit regime, which has now been discontinued.

Under the present framework:

• Section 65 audit is conducted by GST authorities; and
• Section 66 Special Audit is conducted by a CA or Cost Accountant nominated by the Commissioner.

Where a statutory auditor is proposed to provide separate GST advisory, reconciliation or compliance services to the same company, the proposed scope should be examined considering auditor independence, Section 144 of the Companies Act, 2013 and applicable professional requirements.

For a detailed discussion, read Can Statutory Auditor Do GST Audit?.

The Companies Act and related regulatory material can be accessed through the Ministry of Corporate Affairs.

8. Can an Internal Auditor Be Appointed as GST Auditor?

Under the current statutory GST audit framework, this question needs to be considered differently from the earlier turnover-based audit regime.

A departmental audit under Section 65 is conducted by GST authorities, while a Special Audit under Section 66 is undertaken by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

An internal GST compliance review undertaken by a business is separate from these statutory GST audits.

9. Is GSTR-9C Still Certified by a Chartered Accountant?

Under the current framework, GSTR-9C is a self-certified reconciliation statement, wherever applicable.

The earlier requirement involving certification by a Chartered Accountant or Cost Accountant has been removed.

Businesses should therefore not confuse the current GSTR-9C requirement with the earlier GST audit and certification framework.

Returns and forms can be accessed through the official GST Portal.

10. What is an Internal GST Compliance Review?

An internal GST compliance review is a voluntary exercise undertaken by a business to identify GST risks and discrepancies.

It may cover:

• GSTR-1 and GSTR-3B reconciliation;
• GSTR-2B and purchase register reconciliation;
• input tax credit;
• blocked credits;
• reverse charge;
• GST rates;
• HSN/SAC classification;
• place of supply;
• exports and imports;
• e-way bills;
• annual returns; and
• reconciliation with financial statements.

Such a review can help identify potential issues before GST scrutiny or departmental audit.

For a structured review of important GST areas, refer to our GST Audit Checklist.

11. What Records Can Be Checked During GST Audit?

Depending upon the nature of the audit, GST authorities may examine:

• books of account;
• GSTR-1;
• GSTR-3B;
• annual returns;
• input tax credit records;
• GSTR-2B reconciliation;
• sales and purchase registers;
• tax invoices;
• debit and credit notes;
• e-way bills;
• export and import documents;
• financial statements; and
• other relevant records.

The purpose is generally to verify turnover, taxes paid, refunds claimed, input tax credit and overall compliance with GST law.

12. What Should a Business Do After Receiving a GST Audit Notice?

The business should first review the audit period and documents requested in the notice.

It should then prepare relevant GST returns, books, reconciliations and supporting documents and identify any differences before submitting information to the department.

Professional assistance may be useful where the audit involves significant ITC differences, turnover reconciliation, classification issues, exports, reverse charge or other complex transactions.

For assistance, refer to our GST Audit Services in India.

GST Audit – Current Position at a Glance

Departmental Audit – Section 65
Conducted by the Commissioner or an authorised GST officer.

Special Audit – Section 66
Conducted by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

Earlier Turnover-Based GST Audit
Discontinued.

GSTR-9C
Self-certified reconciliation statement, wherever applicable.

Internal GST Compliance Review
Voluntary professional review undertaken to identify GST risks and discrepancies.

Related Services

• GST Audit Services in India – Professional assistance with departmental GST audits, reconciliations, compliance reviews and audit observations.
• Can Statutory Auditor Do GST Audit? – Detailed guidance on statutory auditors and the current GST audit framework.
• GST Audit Checklist – Practical checklist covering GST returns, ITC, reconciliations and documentation.
• Functions of GST Audit Commissionerate – Guidance on GST departmental audit authorities and their functions.
• GST & Indirect Tax Advisory and Litigation Services – Comprehensive GST advisory, audit, assessments, refunds, appeals and litigation assistance.
• Tax and Regulatory Advisory Services in India – Integrated tax and regulatory advisory, compliance and litigation support.

Need Assistance with GST Audit?

EzyBiz India Consulting LLP assists Indian and foreign-owned businesses with GST audit preparation, reconciliations, compliance reviews, responses to audit observations and departmental proceedings.

Prepared By:
EzyBiz India Consulting LLP

Last Updated: August 2026

Disclaimer:
This page provides general information and should not be treated as legal, tax or professional advice. GST provisions, rules and procedures may change, and their applicability should be examined based on the facts and law applicable to each case.