GST Audit Support — Ayyappa Nagar Mogappair & Mogappair

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.

Sub-section (7) of Section 65 provides that where the audit results in detection of tax not paid or short paid, erroneously refunded, or input tax credit wrongly availed or utilised, the proper officer may initiate action under Section 73 or Section 74. It is to be noted that this sub-section is the statutory bridge between the audit conclusion and adjudication proceedings.

Sub-section (4) of Section 65 prescribes that the audit shall be completed within three months from the date of commencement of the audit. The proviso permits the Commissioner, where satisfied that the audit cannot be completed within three months for reasons to be recorded in writing, to extend the period by a further period not exceeding six months. The expression date of commencement is defined in the Explanation to mean the date on which the records and other documents called for by the tax authorities are made available by the registered person, or the actual institution of audit at the place of business, whichever is later.

Sub-section (3) of Section 65 provides that the registered person shall be informed by way of a notice not less than fifteen working days prior to the conduct of audit. The notice is issued in Form GST ADT-01 as prescribed under Rule 101(2). It is to be noted that the fifteen-working-day window is a substantive procedural safeguard; commencement of audit proceedings without compliance with this timeline is a jurisdictional infirmity that may be agitated under Article 226.

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

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.

Comparative framework — VAT/CST audits versus GST audit

Pre-GST, the VAT regime in Tamil Nadu (Tamil Nadu VAT Act 2006) had an audit framework under Section 64 with mandatory CA audit certificates for dealers above prescribed turnover, and the Central Sales Tax framework had limited audit coverage focused on inter-State transactions. The GST framework consolidates and rationalises this — a single audit under Section 65 covers central, State and integrated tax dimensions; the cooperative-federal architecture under Article 246A and 279A means the audit can be conducted by either the central or State authority but not both (Section 6 cross-empowerment). The OECD International VAT/GST Guidelines emphasise audit-efficiency through risk-based selection and digital data analytics, both of which the Indian framework has incorporated through GSTN-driven analytics and the GSTR-9C self-certification feed.

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-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.

Common audit findings

ITC mismatch between GSTR-2A / 2B and GSTR-3B

The single most common Section 65 audit finding is ITC mismatch — ITC claimed in GSTR-3B Table 4(A) exceeding ITC available in GSTR-2A or GSTR-2B for the corresponding tax period. The post-2019 regulatory tightening — Rule 36(4) initially capping un-uploaded ITC at 20%, then 10%, then 5% (Notification 75/2019-CT, 49/2019-CT, 94/2020-CT trajectory), then Section 16(2)(aa) mandating GSTR-2B as the eligibility baseline (Notification 39/2021-CT effective 1 January 2022) — has progressively tightened the mismatch tolerance to nil. Audit findings on FY 2020-21 onwards typically computes the mismatch quarter-wise; the registered person's defence rests on vendor-wise reconciliation, vendor follow-up correspondence, and the Suncraft Energy bona-fide-buyer principle where applicable.

Reverse-charge under Sections 9(3) and 9(4) — self-invoice gaps

The second-most-common audit finding is missed reverse-charge — supplies where the recipient is liable to pay tax under Section 9(3) (notified categories — GTA without forward-charge election, legal services, sponsorship, services by directors, etc.) or Section 9(4) (supplies from unregistered to registered persons in notified categories for real-estate developers under Notification 07/2019-CT(R) read with 03/2019-CT(R)). Section 31(3)(f) requires the recipient to issue a self-invoice; many registered persons miss this step. The audit-team computes the missed output liability under reverse-charge, the corresponding ITC eligibility (subject to time-limit under Section 16(4)), and the interest under Section 50. Voluntary disclosure via DRC-03 is the standard close-out.

Classification and rate-of-tax disputes

The third-recurrent audit finding is classification and rate-of-tax. The GST rate structure across the rate notifications (Notification 01/2017-CT(R) and amendments, Notification 11/2017-CT(R) for services) contains thousands of HSN-and-SAC line items with rates from nil to 28%; classification borderlines are inherent. Audit-team challenges typically focus on: dual-rate items (5%/12%/18% pharmaceutical formulations, footwear, restaurants), composite versus mixed supplies under Section 8 (where the principal-supply classification determines the rate), and works-contract versus pure services classification. The Section 97 Advance Ruling mechanism offers a forward-looking certainty path; for historical classifications, the response is to cite the CBIC circulars (e.g. Circular 164/20/2021-GST on services classification clarifications) and contemporaneous trade-practice evidence.

Pre-audit preparation

Mock audit by independent reviewer

For high-stake audits (multi-year audits, Section 66 special audit nominations, audits of multi-State enterprises), a mock audit by an independent reviewer — typically a former tax-department officer or a senior Chartered Accountant with audit-defence experience — is a useful preparation step. The mock auditor replicates the audit-team's risk-engine-driven interrogation, identifies weak documentary positions, and recommends remedial steps. The cost of mock audits is justified where the potential audit exposure (tax plus interest plus penalty) materially exceeds the mock-audit fee. Comparative income-tax practice has long used mock-audits for high-stake Section 143(3) scrutiny assessments and Section 142(2A) special audits; the GST extension of this practice is recent but growing.

Document marshalling on receipt of ADT-01

Upon receipt of Form ADT-01, the registered person's first task in the fifteen-day window is structured document marshalling. The recommended sequence is: (i) compile the full year's GSTR-1, GSTR-3B, GSTR-2A / 2B downloads; (ii) compile GSTR-9 and GSTR-9C with the underlying reconciliation working papers; (iii) compile sales register, purchase register and stock register from the accounting system; (iv) compile bank statements and cash-book extracts; (v) compile e-way bill summaries; (vi) compile reverse-charge self-invoice register under Section 31(3)(f); (vii) compile Rule 42 / 43 ITC apportionment working papers; (viii) compile statutory audit and tax audit reports for the corresponding financial year. This structured marshalling enables the audit team to verify systematically and shortens the audit cycle materially.

Internal reconciliation walkthrough

Before the audit-team's arrival, the registered person should conduct an internal reconciliation walkthrough — replicating the audit-team's likely interrogation map. The walkthrough should cover: GSTR-1 outward supply versus books turnover; GSTR-3B Table 3.1 versus GSTR-1 invoice-summary; GSTR-3B Table 4(A) ITC claimed versus GSTR-2A / 2B vendor uploads; GSTR-9 Tables 4 to 8 versus GSTR-1 and GSTR-3B aggregates; GSTR-9C Tables 5, 7, 9, 12 to 14 versus audited financial statements. Any variance identified at the walkthrough is an opportunity for voluntary DRC-03 payment before the audit-team formalises it; voluntary disclosure during the walkthrough phase typically attracts no penalty under Section 73(5) read with Section 73(6).

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