Special Audit is a unique provision under GST allowing the department to examine the financials and tax compliance of a taxpayer in greater depth. Unlike regular departmental audits, this is conducted by a professionally qualified external auditor (CA/CMA) when the GST officer suspects:
1. The taxpayer has not correctly declared the value of supplies
2. The taxpayer has availed excess Input Tax Credit (ITC)
3. The structure of transactions is complex
4. There’s a potential loss to revenue

Who is Liable?
This section applies to any registered person under GST:
1. Whose case is under scrutiny, investigation, or inquiry, and
2. Where the Assistant Commissioner (or above) believes a deeper check is required.

Who Will Conduct the Audit?
1. A Chartered Accountant (CA) or Cost Accountant (CMA) will conduct the audit.
2. They are nominated by the GST Commissioner, not chosen by the taxpayer.

Documents Required from Taxpayer
To conduct the audit, the registered person must submit:
1. All Books of Account (Ledger, Cash Book, Purchase & Sales Register)
2. GST Returns (GSTR-1, GSTR-3B, GSTR-9, GSTR-9C)
3. Tax invoices and bills
4. ITC Ledger and reconciliations
5. Bank Statements
6. Contracts, agreements, delivery challans
7. Trial balance, P&L, Balance Sheet
8. Audit Report (if already done under Companies or Income Tax Act)

Non-cooperation may lead to penal consequences under Sections 122–125.

Time Limit for Submission
1. The audit must be completed within 90 days from the date of appointment.
2. The Assistant Commissioner may extend the period once by another 90 days for sufficient reasons.
3. The report must be signed and certified by the nominated professional and submitted to the Assistant Commissioner.

Section 65 vs. Section 66 – Key Differences