GST Audit Support in Koyambedu Flower Market, Chennai

Sub-section (1) of Section 65 of the Central Goods and Services Tax Act empowers the Commissioner, or any officer authorised by him through a general or specific order, to undertake audit of any registered person for such period, frequency and manner as may be prescribed. Sub-section (2) provides that the audit may be conducted either at the place of business of the registered person or at the office of the proper officer. It is to be noted that this provision is the substantive source of departmental audit jurisdiction and is read with Rule 101 for procedural mechanics.

Sub-section (1) of Section 66 provides that if at any stage of scrutiny, inquiry, investigation or any other proceedings, the officer not below the rank of Assistant Commissioner, having regard to the nature and complexity of the case and the interest of revenue, is of the opinion that the value has not been correctly declared or the credit availed is not within the normal limits, he may, with prior approval of the Commissioner, direct the registered person to get the records including books of account examined and audited by a chartered accountant or a cost accountant nominated by the Commissioner.

Sub-rule (1) of Rule 101 provides that the period of audit shall be a financial year or part thereof or multiples thereof. Sub-rule (2) prescribes Form GST ADT-01 for the audit notice. Sub-rule (4) directs the proper officer, on conclusion of audit, to record the audit observations in his audit notes and to inform the registered person of the discrepancies, who may file his reply. Sub-rule (5) prescribes Form GST ADT-02 for communication of audit findings.

Section 36 directs every registered person required to keep and maintain books of account or other records under sub-section (1) of Section 35 to retain them until the expiry of seventy-two months from the due date of furnishing the annual return for the year pertaining to such accounts and records. It is to be noted that where the records pertain to a matter that is the subject of an appeal, revision or any other proceeding, retention is required until one year after final disposal.

Sub-section (6) of Section 65 requires the proper officer, on conclusion of audit, to inform the registered person within thirty days of the findings, the registered person's rights and obligations, and the reasons for such findings. The communication is issued in Form GST ADT-02. It is to be noted that the thirty-day window is mandatory and starts on the date of conclusion of audit, not the date of the audit report.

Sub-section (2) of Section 66 provides that the direction under sub-section (1) shall be issued in Form GST ADT-03 as prescribed under Rule 102. The nominee chartered accountant or cost accountant is named by the Commissioner; the registered person does not have a right to choose the auditor. It is to be noted that this is materially different from the statutory audit framework under the Companies Act where the management appoints the auditor.

What is a GST audit and where does it sit in the compliance architecture

Statutory framework under Chapter XIII of the CGST Act

The audit framework under the Central Goods and Services Tax Act 2017 is contained in Chapter XIII, comprising Sections 65, 66 and 71. Section 65 provides for departmental audit, Section 66 for special audit by a Chartered Accountant or Cost Accountant nominated by the Commissioner, and Section 71 for access to business premises by an authorised officer. The Empowered Committee 2009 First Discussion Paper had envisaged audit as the principal verification layer in a self-assessment regime, replacing the pre-GST pattern of routine assessment under the VAT/CST framework. The architecture is risk-based: not every registered person is audited; selection is driven by Section 65(2) read with internal CBIC risk-management directions which factor in turnover scale, sectoral risk profile, prior compliance history and reconciliation gaps surfaced in GSTR-9C self-certification. The audit-process closure under Section 65(7) feeds either into a no-objection certificate, a voluntary DRC-03 payment, or an SCN under Section 73 or Section 74 depending on whether tax has been short-paid, short-collected or wrongly availed as ITC.

Audit versus assessment versus inspection

Audit under Section 65 or 66 is conceptually distinct from assessment under Sections 61 (scrutiny of returns) and 62 (best-judgement assessment of non-filers) and from inspection / search / seizure under Section 67. Scrutiny under Section 61 is a desk-review of returns by the proper officer who issues ASMT-10 on discrepancies; the registered person responds in ASMT-11; closure or escalation follows. Audit is broader — Section 65(5) permits examination of the books, returns, statements, declarations and other documents to verify correctness of turnover declared, taxes paid, refund claimed and ITC availed, plus assessment of compliance with the Act. Inspection under Section 67 is targeted enforcement upon reason-to-believe of tax evasion and is invasive — premises access, seizure of records and goods. The OECD Forum on Tax Administration's compliance-pyramid model recommends graduated escalation from desk review to field audit to inspection, and the Indian framework broadly mirrors that design.

Self-certification under GSTR-9C and its audit interplay

Until Finance Act 2021 amendments, Section 35(5) had required certification of GSTR-9C by a Chartered Accountant or Cost Accountant for registered persons whose aggregate turnover exceeded the prescribed threshold. The Finance Act 2021 substituted Section 35(5) and amended Section 44, shifting GSTR-9C to a self-certified reconciliation statement filed by the registered person without third-party attestation, effective FY 2020-21 onwards (Notification 29/2021-CT). The reconciliation in GSTR-9C between audited financial statements and GSTR-9 annual return is now an internal-control disclosure; it does not substitute for departmental audit under Section 65. Audit teams treat GSTR-9C self-certified reconciliations as primary working papers — Table 5 (turnover reconciliation), Table 9 (tax payable reconciliation) and Table 12-14 (ITC reconciliation) become the starting points of Section 65 audit interrogation.

GSTR-9C self-certification interplay with audit

Optional GSTR-9C and tactical considerations

For registered persons whose aggregate turnover is between ₹2 crore and ₹5 crore (where GSTR-9 is optional under Notification 47/2019-CT and similar; GSTR-9C threshold is above ₹5 crore), the strategic question is whether to file GSTR-9 and GSTR-9C voluntarily. Voluntary filing provides a contemporaneous reconciliation record that strengthens the audit-defence position; non-filing leaves the audit team to compute reconciliation themselves from primary records, often less favourably. The GST Council 47th Chandigarh and 53rd meetings have periodically rationalised these thresholds; the Empowered Committee 2009 First Discussion Paper had envisaged annual-return-as-integrating-layer architecture that the current threshold-based structure has partially diluted.

Self-certification regime from FY 2020-21

Notification 29/2021-CT and the Finance Act 2021 substitution of Section 35(5) shifted GSTR-9C from CA / CMA attested certification to self-certification by the registered person, effective from financial year 2020-21 onwards. The reconciliation statement now bears the signature of the registered person or the authorised signatory; the previous Part B CA-CMA certification has been dropped. The substantive contents of GSTR-9C — Part A (reconciliation between audited financial statements and GSTR-9, covering turnover Table 5, taxable value Table 7, tax payable Table 9, ITC Tables 12-14) and Part B (auditor certification, now omitted) — are otherwise broadly retained. The threshold for GSTR-9C continues to be aggregate turnover above ₹5 crore, per Notification 16/2022-CT.

GSTR-9C as audit working paper

From the Section 65 audit-team perspective, GSTR-9C is the primary working paper that drives initial audit-topic selection. Table 5 turnover reconciliation surfaces unbilled-revenue, advance-receipt and inter-State stock-transfer issues. Table 7 taxable-value reconciliation surfaces classification and exemption-claim issues. Table 9 tax-payable reconciliation triggers rate-of-tax interrogation. Tables 12 to 14 ITC reconciliation drive Section 16 eligibility and Rule 42 / 43 apportionment audits. The audit team treats unexplained variances in any of these tables as priority interrogation topics; the registered person's strongest defence is a contemporaneous explanatory note attached to GSTR-9C addressing each material variance. CBDT Circular 8/2021 (in the AIS context, on reconciliation principles) and CBIC Circular 124/43/2019-GST on GSTR-9C format offer guidance.

Section 67 inspection and its relation to audit

Procedural safeguards under Section 67(2) to 67(10)

Section 67(2) requires that search and seizure shall be carried out in the manner prescribed under Rule 139; provisions of the Code of Criminal Procedure 1973 relating to search and seizure apply mutatis mutandis (Section 67(10)). Section 67(7) provides that goods so seized shall be returned within six months extendable by six months for sufficient reasons. Section 67(8) preserves the registered person's right to make copies of the seized documents. The procedural safeguards exist; the OECD Forum on Tax Administration recommends similar safeguards as part of the taxpayer-rights framework. In practice, the Bharti Airtel v UoI and Suncraft Energy v Asst Commissioner lines of authority have shaped the procedural-fairness review of Section 67 actions in writ jurisdiction before the Madras High Court and other High Courts.

Comparative framework — pre-GST excise / service tax and current GST

Pre-GST, the Central Excise Act Section 14 provided summons power, Section 18 search power, and Section 12F seizure power. Service tax under the Finance Act 1994 had similar provisions under Sections 82 (search) and 73 (recovery). The GST framework consolidates these into Section 67 with unified procedural architecture. The Empowered Committee 2009 First Discussion Paper had envisaged a single-window enforcement architecture replacing the fragmented pre-GST regime; Section 67 substantively delivers that design. Comparative OECD International VAT/GST Guidelines emphasise that enforcement powers should be calibrated to the gravity of the suspected evasion, and the Indian framework's reason-to-believe-plus-Joint-Commissioner-rank gating mechanism aligns with that principle.

Section 67 framework and reason-to-believe trigger

Section 67 of the CGST Act empowers the proper officer not below the rank of Joint Commissioner, upon reasons to believe recorded in writing, to inspect any place of business of a taxable person or any other person engaged in the business of transporting goods or owner or operator of a warehouse or godown, and to search and seize goods, documents, books and things. The Section 67 power is enforcement-oriented, triggered by suspicion of tax evasion (suppression of supply, claim of ITC in excess of entitlement, contravention of Act or rules), and is distinct from the verification-oriented Section 65 audit. The audit-to-inspection escalation occurs where Section 65 audit finds material gravity that the proper officer reads as warranting enforcement action under Section 67.

Audit-to-DRC-01 escalation

Defending Section 74 fraud framing

Where the audit-team recommends Section 74 framing, the registered person's defence focuses on the four elements — fraud, wilful misstatement, suppression of facts, or contravention with intent to evade tax. The Supreme Court's pre-GST jurisprudence on similar language in Central Excise (Pushpam Pharmaceuticals v CCE) and Service Tax (CCE v Mehta and Co) emphasised that mere non-payment or non-disclosure does not amount to suppression with intent; positive indicators of intent are needed. Bona-fide classification errors, computational mistakes, and reasonable interpretation differences are not suppression. Where the SCN frames the case under Section 74, the response should systematically address each of the four elements and rely on the documentary trail showing bona-fide compliance attempts. Pradeep Goyal (DIN requirement) and Kranti Associates (reasoned order) provide procedural safeguards.

Limitation analysis post audit

Section 73(10) provides that the order under Section 73 shall be issued within three years from the due date for furnishing of annual return for the financial year to which the tax not paid or short paid or input tax credit wrongly availed relates; the SCN must be issued at least three months before that date (Section 73(2)). Section 74(10) provides corresponding five-year limitation. For FY 2017-18 GSTR-9 (annual return due 31 December 2018, extended dates apply), the Section 73 limitation expired in late 2021-22 (extended through various Notifications including 9/2023-CT to 31 December 2023 and further), and Section 74 limitation extends to mid-2024 onwards. Audit findings escalated beyond limitation are barred; the registered person should systematically test limitation as part of the SCN defence.

Appellate framework — Section 107 first appeal and beyond

Where the Section 73 or 74 adjudication order under DRC-07 is adverse, the registered person's first appeal lies under Section 107 of the CGST Act before the Joint or Additional Commissioner (Appeals) within three months from the date of communication of the order, extendable by one month for sufficient cause. Pre-deposit of 10% of the disputed tax amount under Section 107(6) is the gateway requirement. Second appeal lies under Section 112 before the GST Appellate Tribunal (now operational with Principal Bench at New Delhi and State / Area Benches notified); the Section 112 pre-deposit is an additional 20% (cumulative 30%). Beyond the Tribunal, appeal lies to the High Court under Section 117 on questions of law, and to the Supreme Court under Section 118. Writ remedy under Article 226 of the Constitution before the Madras High Court is available for jurisdictional infirmities at any stage.

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Three-year audit period closed in 47 days against the Section 65(4) ceiling of 90 working days

Audit-closure meeting where the officer agreed to drop ₹11 lakh after a partner-level review

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