GST Assessment vs Audit in 2026: Sections 59–66 and What Each One Triggers

Six routes, not one — the GST law's assessment architecture

If you are GST-registered, the law gives the department six distinct routes to look at your numbers. Each has its own form, its own trigger, its own time limit, and its own consequence. Confusing them is one of the most common reasons a routine query becomes a recovery proceeding.

This guide walks through Sections 59 to 66 of the CGST Act, 2017 — the six routes — and explains when each one applies in practice.

Section 59 — self-assessment

The default. Under Section 59 of the CGST Act, every registered person assesses the tax payable on the supplies they make, and pays it through the periodic return. The whole compliance machinery — GSTR-1, GSTR-3B, GSTR-9, payment via electronic cash and credit ledgers — runs on self-assessment. The other five routes are exceptions that arise when self-assessment is incomplete, late, or contested.

Section 60 — provisional assessment

Used when the taxpayer is genuinely unable to determine the value or rate of a supply. Under Section 60, the registered person applies in Form GST ASMT-01 for permission to pay tax on a provisional basis; the proper officer issues ASMT-04 allowing or rejecting it, possibly against a bond and security.

The final assessment under ASMT-07 must be passed within six months of the provisional order, extendable by the Joint/Additional Commissioner by a further six months and by the Commissioner by a further period not exceeding four years; the outer limit is therefore five years — a long enough window that provisional assessment is rare in practice but useful in genuinely uncertain situations (a new product line, a disputed classification awaiting clarification).

Section 62 — best-judgment assessment of a registered non-filer

If a registered person fails to file the return required under Section 39 or 45 even after a notice in Form GST GSTR-3A, the proper officer may proceed under Section 62 and assess the tax liability to the best of judgment, taking into account the information available. The order is in Form GST ASMT-13.

The crucial escape hatch in Section 62(2): if the registered person furnishes a valid return within sixty days of the service of the assessment order — extendable by another sixty days on payment of additional late fees — the assessment order under Section 62 is deemed to have been withdrawn. The interest and late fees still apply, but the assessed liability falls away. Filing the missing return promptly is almost always cheaper than letting the best-judgment liability stand.

Section 63 — best-judgment assessment of an unregistered person

For a person liable to register but not registered, or whose registration was cancelled but who was liable to pay tax, Section 63 empowers the proper officer to assess to the best of judgment. A notice in Form GST ASMT-14 is issued, the person is allowed fifteen days to file a reply, and an order is passed in Form GST ASMT-15. The exposure period can run up to five years from the date specified under Section 44 for furnishing the annual return for the financial year to which the unpaid tax relates.

For a Pune service business that crossed the ₹20 lakh threshold in March 2026 but registered only in November, the unregistered period (April–October) sits under Section 63. The cleanest defence is voluntary registration the moment the threshold is crossed — see our GST Registration Guide 2026.

Section 64 — summary assessment in special cases

A fast-track route under Section 64 when the proper officer has evidence that a person is liable to tax and any delay in raising the demand will adversely affect revenue. With prior permission of the Additional/Joint Commissioner, an order is passed in Form GST ASMT-16. The person can apply for withdrawal in ASMT-17 if the order is found to be erroneous; the order under Section 73 or 74 may follow if circumstances warrant.

Summary assessments are rare and typically used where there is fly-by-night risk — a person making large supplies and disappearing.

Section 65 — regular audit by tax authorities

The most common touchpoint after scrutiny. Under Section 65 read with Rule 101 of the CGST Rules:

• A notice in Form GST ADT-01 is issued before commencement, generally fifteen working days in advance.
• The audit covers a financial year or part thereof, or multiples thereof (Rule 101(1)).
• The audit is to be completed within three months from the date of commencement; the Commissioner may extend the period by a further period not exceeding six months for reasons recorded in writing (Section 65(4)).
• The auditee must furnish necessary information and records; "commencement" means the date on which records called for are made available, or the actual institution of audit at the place of business, whichever is later.
• On conclusion, the findings are intimated in Form GST ADT-02 to the registered person under Section 65(6), with reasons.

If the audit reveals tax not paid or short-paid, ITC wrongly availed, or refund wrongly given, the proper officer initiates action under Section 73 or 74 — i.e. a show-cause notice and recovery. The 73(5)/74(5) safe harbour (no penalty if paid before SCN) applies here too.

Section 66 — special audit by a chartered accountant or cost accountant

Where the proper officer, at any stage of scrutiny, inquiry, investigation or other proceedings, has reason to believe that the value has not been correctly declared or the credit availed is not within normal limits, Section 66 allows him — with prior approval of the Commissioner — to direct a registered person to get their records audited by a nominated chartered accountant or cost accountant.

The direction is in Form GST ADT-03. The CA/CMA submits a report within ninety days of the direction, extendable by ninety days. The findings are intimated to the registered person in Form GST ADT-04. Importantly, the expenses and remuneration of the special auditor are determined and paid by the Commissioner, not the auditee — though the audit itself can be intrusive and disruptive.

A special audit under Section 66 typically follows a scrutiny notice the department considers serious, or a sectoral concern (high-value B2B credit chains, common-input apportionment in real-estate or financial services).

How the six routes sit alongside each other

A clean compliance posture — timely filing, AIS-like reconciliation between GSTR-1, 3B and 2B every month, RCM cash payment, e-way bill discipline — keeps you firmly in Section 59 territory. The other five sections are exceptions, and they all have escape hatches built in if you act promptly.

Audit vs assessment in practice — three Pune scenarios

Scenario A — Pune manufacturer with steady GSTR-3B and GSTR-1. Self-assessment under Section 59. No further engagement unless a discrepancy surfaces.

Scenario B — Pune trader who missed three months of returns. Notice in GSTR-3A; if no response, Section 62 best-judgment in ASMT-13. Filing the missing returns within 60 days deems the order withdrawn under Section 62(2).

Scenario C — Pune professional crossed ₹20L threshold three quarters ago, still not registered. Section 63 territory. Voluntary registration immediately, then ASMT-14 reply if the notice has been issued, with the unregistered-period tax paid in DRC-03 with interest.

For the scrutiny step that sits between self-assessment and these escalations, see our guide to the Form ASMT-10 scrutiny notice reply; for the registration mechanics that prevent Section 63 exposure, see the GST Registration Guide 2026.

Pune note: where we step in for an ADT-01 or ASMT-13

At RDA Tax Advisory Services, Baner, we handle the full assessment-and-audit lifecycle for Pune businesses. For Section 65 departmental audits, we coordinate the records list called for in ADT-01, run the pre-audit reconciliation so the auditor finds reconciliations rather than discrepancies, and represent the auditee through the findings stage. For Section 62 best-judgment cases, we file the missing returns within the 60-day window to secure the deemed-withdrawal benefit. For Section 63 unregistered-period exposure, we register, file ASMT-14 replies and prepare the DRC-03 cash payment with Section 50 interest. Office No. 102, Snehraj Apartment, Baner, Pune 411045 · call +91 77570 45059.

Got an ADT-01, ASMT-13 or ASMT-14?

Pune business under GST audit or facing a best-judgment notice? Forward the notice on WhatsApp; we read the section, identify the route, prepare the reconciliation and reply within the deadline. Book a GST audit consult at rdatax.in or call +91 77570 45059 — RDA Tax Advisory Services, Baner, Pune.

Verification note: Material legal positions in this article — Section 59 (self-assessment), Section 60 (provisional, ASMT-01/04/07 forms, 6-month + 6-month + 4-year window), Section 62 (registered non-filer, ASMT-13, 60-day withdrawal under Section 62(2)), Section 63 (unregistered, ASMT-14/15, 15-day reply window, 5-year exposure), Section 64 (summary, ASMT-16), Section 65 (audit, ADT-01/02, financial-year or part period under Rule 101, 3-month + 6-month time limit under Section 65(4), Section 65(6) intimation in ADT-02), and Section 66 (special audit, ADT-03/04, 90-day report extendable by 90 days, expenses paid by the Commissioner) — are sourced from the CBIC Tax Information Portal text of the CGST Act, 2017 and CGST Rules, 2017. Confirm specific facts with your CA.