GST Audit Support in MEPZ-Tambaram SEZ, 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.

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.

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 (5) of Section 65 obliges the registered person to afford the necessary facility to verify the books of account or other documents as may be required, and to furnish such information as may be required and render assistance for timely completion of the audit. It is to be noted that non-cooperation under this sub-section can lead the proper officer to invoke best-judgment assessment under Section 62 or escalate to special audit under Section 66.

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.

ADT-03 cost recovery

Determination of remuneration and challenges

The Commissioner determines the remuneration of the nominated Chartered Accountant or Cost Accountant under Section 66(4) based on rates broadly aligned with the ICAI and ICMAI minimum recommended scales for special-audit work. The registered person typically has no direct say in either the selection of the CA/CMA or the remuneration determination — both are administrative decisions of the Commissioner. Challenges to ADT-03 cost-recovery are rare in practice and usually focus on the underlying Section 66 nomination itself rather than the quantum. Where the Section 66 nomination was procedurally infirm (no Commissioner approval, no opportunity of being heard, no recorded reasons), the consequential ADT-03 cost-recovery similarly becomes vulnerable in writ proceedings. The OECD Forum on Tax Administration documents this cost-recovery pattern as common across jurisdictions that use specialist-audit tiers.

Payment timeline and Section 79 recovery framework

Once ADT-03 is served, the cost-recovery amount becomes payable within the timeline specified in the form (typically thirty days). Non-payment triggers Section 79 of the CGST Act — the Government dues recovery framework — which empowers the proper officer to recover the amount through modes including deduction from any amount due to the registered person, sale of any movable or immovable property, attachment of bank accounts under Section 83 provisional attachment, and recovery as land revenue arrears. The registered person can apply for instalment-payment under Section 80 read with Rule 158 where genuine financial hardship exists; the Commissioner has discretion to allow up to twenty-four monthly instalments subject to interest under Section 50.

Cost-recovery in practice — pattern from Tamil Nadu Commissionerates

In practice, ADT-03 cost-recovery determinations issued by Tamil Nadu Commissionerates have ranged from modest amounts (₹50,000-₹2 lakh for limited-scope special audits) to substantial amounts (₹10 lakh and above for multi-year complex audits involving multiple GSTINs). The pattern correlates with the audit-scope — broad valuation or ITC-eligibility audits at large multi-State entities typically yield higher cost-recovery quantums. Registered persons under Section 66 nomination are well-advised to engage with the CA/CMA on a documented scope-limitation memorandum to control the quantum; reasonableness of the determination is reviewable in writ jurisdiction though the threshold for interference is high.

Records retention under Section 35

Statutory framework and retention horizon

Section 35(1) of the CGST Act requires every registered person to keep and maintain, at his principal place of business and at every additional place of business mentioned in the certificate of registration, a true and correct account of production or manufacture of goods, inward and outward supply of goods or services or both, stock of goods, input tax credit availed, output tax payable and paid, and such other particulars as may be prescribed. Section 36 mandates that every registered person required to keep books and accounts under Section 35 shall 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. The seventy-two-month (six-year) retention horizon aligns with the Section 73 normal-period limitation of three years from the due date of the annual return, and the Section 74 extended-period limitation of five years, with a safety margin.

Specific records prescribed under Rules 56 to 58

Rule 56 of the CGST Rules elaborates the records to be maintained under Section 35 — accounts of goods or services received and supplied, stock of goods (with opening balance, receipt, supply, goods lost stolen destroyed written off or disposed of by way of gift or free sample, balance), particulars of ITC availed, output tax payable and paid, names and complete addresses of suppliers and customers, complete addresses of premises where goods are stored including goods stored during transit, monthly production accounts (for manufacturers) showing quantitative details of raw materials and goods produced, and accounts of advances received and paid. Rule 57 provides for maintenance through electronic means with prescribed safeguards. Rule 58 covers transporter, owner and operator of warehouse records. The records-architecture is granular and audit teams systematically map registered-person records against the Rule 56 schema during Section 65 audits.

Consequences of failure to maintain records

Failure to maintain accounts and records as prescribed under Section 35 read with Rule 56 attracts consequences under multiple provisions. Section 35(6) empowers the proper officer to determine the tax payable on the goods or services or both not accounted for as if such goods or services or both had been supplied by such person, and the provisions of Sections 73 or 74 shall apply for determination of such tax. Section 122 provides for penalty for various offences including failure to maintain records — up to ₹10,000 or the amount of tax evaded, whichever is higher. The audit team's working assumption in cases of inadequate records is that the burden shifts to the registered person to demonstrate the correctness of declared turnover and ITC; this evidentiary shift is the most material consequence in practice.

Rule 56 stock records

Sectoral application of Rule 56(18) — jewellery, precious metals

Rule 56(18) applies to a narrow but high-revenue-risk band of trades — precious metals, precious stones, jewellery — where stock-record granularity is essential because of the high unit-value and pilferage-risk profile. The daily quantity-wise register must capture purity (in carats for gold), weight (in grams or pennyweights), make-charges component, hallmarking certificate references (BIS hallmark unique identification), and customer-wise sale-bill traces. Family-run jewellery businesses in particular often default to consolidated weekly or monthly stock summaries; this gap is the most common audit finding in jewellery-sector Section 65 audits in Tamil Nadu. Coordinated compliance with TCS under Section 206C(1F) at 1% on sales above ₹2 lakh adds an income-tax overlay to the stock-records architecture.

Stock-record obligations under Rule 56(2) and Rule 56(18)

Rule 56(2) of the CGST Rules requires every registered person, other than a person paying tax under Section 10 (composition), to maintain accounts of stock in respect of goods received and supplied — showing opening balance, receipt, supply, goods lost, stolen, destroyed, written off or disposed of by way of gift or free sample, and balance of stock including raw materials, finished goods, scrap and wastage. Rule 56(18) imposes a higher-granularity obligation on registered persons dealing in goods of the kinds notified — currently primarily precious metals, precious stones and jewellery — requiring daily quantity-wise and value-wise stock registers. The granularity differential between Rule 56(2) and Rule 56(18) reflects the sector-specific revenue-risk assessment that has been part of Indian indirect-tax administration since pre-GST excise.

Reconstruction of stock records during audit

Where stock records under Rule 56(2) are incomplete or absent — a common scenario in SME manufacturing and trading — reconstruction during the ADT-01 fifteen-day window is the standard response. The reconstruction sources include purchase invoices and GSTR-2A entries (for inward stock), GSTR-1 outward supplies (for sales), e-way bill data (for stock movements), bank statements (for cash purchases or sales not invoiced through GST channels), and stock-take working papers from the statutory audit under the Companies Act or Section 44AB income tax audit. Reconstruction must be contemporaneous with the original transaction dates; backdated reconstruction is treated as fabrication by the audit team. The Tapas Dutta v UoI line of authority on retrospective records is occasionally invoked, but registered persons should not rely on it as a safe harbour.

Bharti Airtel rectification doctrine used to correct GSTR-3B at audit for a {{area_name}} engineering firm

Section 65 audit on transition credit defended for a {{area_name}} engineering firm

Rule 56(1) ledger gap of seven months — reconstructed from bank and e-invoice in eight days

Table 8D adverse finding of ₹47 lakh cured before ADT-02 by re-running the 2B match

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