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GST Health Check Services
A GST Health Check is a structured, diagnostic review of a taxpayer's end-to-end GST position — designed to proactively identify errors, leakages, exposures, and grey-area risks before they are surfaced by the tax department through a Section 61 scrutiny notice, Section 65 departmental audit, DRC-01A / 01B / 01C intimation, or a full-scale Section 73 / 74 proceeding. Unlike statutory GSTR-9C reconciliation, which is limited in scope and annual in cadence, a Health Check is an independent, advisory-led exercise spanning multiple financial years that goes deeper into classification, rate, ITC, RCM, cross-charge, export, refund, e-invoice, e-way bill, and documentation hygiene — covering every GSTIN of the group across states, entities, and business lines.
A well-designed GST Health Check tests substance and documentation on the provisions that matter most in real-world assessments — Section 16 and Rule 36(4) for ITC eligibility, Section 17(5) for blocked credits, Rule 42 / 43 for exempt / common credit reversals, Section 9(3) / 9(4) for RCM, Section 15 and Rules 27–35 for valuation, Sections 10 / 12 / 13 for place and time of supply, Section 34 and the November 30 cut-off for credit notes, Section 29(5) and Rule 44 for stock-on-cancellation, Rule 48(4) for e-invoicing, Section 16 IGST with Rule 96 / 96A for exports and refunds, and Rule 21A / Rule 138E for suspension and E-Way Bill blocking. Every theme is tested not as a tick-box but as a genuine audit-grade enquiry — sample-based, evidence-driven, and risk-rated.
Our GST Health Check Services deliver a comprehensive, issue-wise report covering every material GST position of the group — each issue graded as High / Medium / Low risk, with recommended corrective actions (file amendments, reverse ITC via DRC-03, strengthen documentation, re-classify, issue credit notes, amend contracts, redesign ERP logic, or take an Advance Ruling) — so that the client can close gaps, recover leakage, and walk into any future departmental audit, scrutiny, or M&A due diligence with clean, defensible, well-documented GST records.
50+ Check Points
Per GSTIN review
Multi-Year
Typically 3-5 years
Risk-Rated
High / Medium / Low
Pre-Audit
Before ADT-01 arrives
Laws & Provisions We Test
CGST Act – Sec 15 / 16 / 17
CGST Act – Sec 31 / 34 / 35
CGST Act – Sec 9(3) / 9(4)
CGST Act – Sec 73 / 74 Risk
CGST Rules – Rule 36(4) / 42 / 43
CGST Rules – Rule 48(4)
IGST Act – Sec 10 / 12 / 13 / 16
Rule 96 / 96A / 138E
Main Review Areas in Our GST Health Check
Outward
Outward Supplies & Revenue
Classification, rate, valuation, place / time of supply, exemptions, and revenue reconciliation.
- HSN / SAC & rate testing
- POS determination
- Composite / mixed supply
- Discounts & Sec 15(3)
- Schedule I / II / III
- Books vs GSTR-1 tie-out
ITC
Input Tax Credit Review
Deep review of ITC eligibility, Section 17(5) blocked credits, and Rule 42 / 43 reversals.
- Section 16 conditions
- GSTR-2B vs books
- Rule 36(4) compliance
- Blocked credits (17(5))
- Common credit reversal
- Capital goods tracking
RCM & ISD
RCM, ISD & Cross-Charge
Review of reverse charge, cross-charge between distinct persons, and ISD credit distribution.
- Sec 9(3) notified supplies
- URD RCM under 9(4)
- Self-invoicing
- Cross-charge workings
- ISD Rule 39 compliance
- Schedule I testing
Exports
Exports, SEZ & Refunds
Review of LUT, Rule 96A timelines, IGST refunds, and ITC refund under Rule 89.
- LUT coverage
- 3-month / 1-year check
- Shipping bill matching
- FIRC / BRC review
- Refund optimisation
- Deemed exports
Documentation
Invoice & Document Hygiene
Testing of invoice series, Rule 46 particulars, e-invoice coverage, and credit / debit notes.
- Rule 46 particulars
- IRN coverage & QR
- Delivery challan use
- Credit note 30-Nov cut-off
- Revised / self-invoice
- Record retention
Operational
E-Way Bill & Operational Risk
E-Way Bill coverage, Rule 138E blocking risk, MOV exposure, and suspension risk under Rule 21A.
- EWB vs invoice match
- EWB vs IRN match
- Validity lapses
- Rule 138E blocking
- Rule 21A suspension risk
- MOV exposure review
Key Risk Themes We Test at a Glance
Rate Risk
Classification & Rate
Incorrect HSN / SAC leading to short payment of output tax or denial of concessional rate.
Output Tax
Refund
ITC Leakage
Rule 36(4) & 2B Gaps
ITC claimed without matching GSTR-2B, Section 16(2)(aa) / (ba) non-compliance.
2B Mismatch
Interest 18%
Blocked Credit
Section 17(5)
Ineligible ITC on motor vehicles, food, construction, and other blocked categories.
17(5)
Reversal
RCM Gaps
Section 9(3) / 9(4)
Missed RCM on GTA, advocates, security services, and notified URD procurements.
GTA
URD
Cross-Charge
Distinct Persons
Missed cross-charge between branches of the same PAN across states — Schedule I supplies.
Schedule I
Branches
Credit Note
November 30 Cut-Off
Credit notes not reported by Sec 34(2) cut-off, resulting in permanent loss of GST adjustment.
Sec 34
Time Bar
Export
Rule 96A Timelines
Exports not completed in 3 months or realisation beyond 1 year — IGST + interest exposure.
3 Months
1 Year
E-Invoice
Rule 48(4) / 48(5)
Invoices without IRN where applicable — buyer-side ITC risk and Section 122 penalty.
IRN
Invalid Inv
What Our Health Check Engagement Covers
Scoping
Scoping & Data Room
Engagement scoping, period selection, GSTIN / entity mapping, and data room setup.
- GSTIN inventory
- Period selection
- Data request list
- Sampling methodology
- Confidentiality & NDA
- Kick-off walkthrough
Review
Issue-Wise Testing
Execution of the check-point matrix across outward, ITC, RCM, exports, and documentation.
- Outward supply testing
- ITC & 2B reconciliation
- RCM / ISD / cross-charge
- Export & refund review
- E-invoice / EWB hygiene
- Record retention check
Report
Report & Remediation
Risk-rated report with recommended actions, quantum, and remediation roadmap.
- Executive summary
- Issue-wise findings
- Quantum estimation
- Risk rating (H / M / L)
- Action plan
- DRC-03 strategy
Our GST Health Check Services
Full-Scope Diagnostic
Complete 50+ check-point review across every pillar — outward, ITC, RCM, exports, and documentation.
ITC Health Check
Focused review of ITC eligibility, 2B reconciliation, 17(5) blocked credits, and 42 / 43 reversals.
Pre-Audit Review
Rehearsal of a Section 65 audit before ADT-01 — data room, sampling, and narrative defence.
M&A Due Diligence
Buy-side or sell-side GST due diligence in slump sale, demerger, and share / asset transactions.
Multi-GSTIN Group Review
Coordinated review across GSTINs, branches, and entities of a group with consolidated MIS.
Sector-Specific Review
Targeted review for real estate, hospitality, BFSI, healthcare, e-commerce, and works contract.
Refund & LUT Review
Focused review of export / SEZ / inverted-duty refund pipeline, LUT coverage, and leakage recovery.
Remediation & DRC-03
Assisted remediation with DRC-03 voluntary payments, credit notes, and process redesign.
When You Need a GST Health Check
Section 65 Audit Coming
Advance intelligence or sector trend suggests an ADT-01 audit in the near term.
M&A / Investment Round
Planned transaction — buy-side, sell-side, PE / VC round, or IPO — needs a clean GST position.
Prior Notices / Disputes
Earlier ASMT-10, DRC-01B / 01C, or DRC-01 exposure calling for a pre-emptive clean-up.
Multi-State / Multi-GSTIN
Group with several GSTINs across states needing consistent positions and no hidden surprises.
New Management / CFO
New finance leadership wanting an independent, written view on the GST position inherited.
Significant Refund Pipeline
Large export / SEZ / inverted-duty refunds pending — leakage-free claim strategy required.
E-Invoicing Go-Live
Recently crossed threshold — data hygiene from the pre-IRN period needs to be reconciled.
Board / Audit Committee Ask
Board or audit committee wants an independent GST risk opinion for governance purposes.
Information & Documents Needed
Returns & Ledgers
- GSTR-1 / 3B / 2A / 2B
- GSTR-9 / 9C
- Electronic cash & credit ledger
- DRC-03 / PMT-06
- LUT / bond copies
- Refund applications
- Prior notices / orders
Books & Financials
- Audited financials
- Trial balance & ledger
- Tax audit report (3CD)
- Sales & purchase registers
- Stock & FA registers
- RCM / ISD workings
- Cost audit report
Operational & Evidence
- Sample tax invoices
- Contracts & POs
- E-invoice / IRN data
- E-Way Bill data
- Export / FIRC / BRC
- HSN / SAC mapping
- ERP / billing config
Our End-to-End Health Check Approach
1
Scoping
Scoping workshop to define GSTINs, periods, entities, and review depth.
2
Data & Walkthroughs
Data room setup, process walkthroughs, and master data review.
3
Testing
Issue-wise testing across 50+ check points with sampling and evidence documentation.
4
Report
Risk-rated report with quantum, root cause, and recommended remediation.
5
Remediation
Assisted remediation — DRC-03, amendments, credit notes, process redesign, ERP change.
Why Choose Our GST Health Check
✓
50+ check-point diagnostic depth
✓
Senior CA-led engagement
✓
Risk-rated findings (H / M / L)
✓
Quantum-backed recommendations
✓
ITC leakage recovery
✓
Pre-audit defence readiness
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Sector-specific insight
✓
Board-ready reporting
FAQs on GST Health Check
What is a GST Health Check and how is it different from statutory audit?
A GST Health Check is an independent, advisory-led diagnostic review of the taxpayer's end-to-end GST position — designed to proactively identify errors, leakages, and exposure areas before they are detected by the tax department. It is materially broader and deeper than statutory reconciliation in Form GSTR-9C, which is confined to tying the books with filed returns and is annual in scope. A Health Check instead spans multiple financial years, tests advisory positions on rate, classification, RCM, cross-charge, 17(5) blocked credits, Rule 42 / 43 reversals, LUT timelines, and e-invoice coverage, and delivers a risk-rated written report with specific corrective actions. It is voluntary, confidential, and entirely under the client's control — unlike a Section 65 departmental audit, which is statutorily mandated and adversarial in nature.
How long does a GST Health Check engagement typically take?
Duration depends on the scope, number of GSTINs, years covered, and complexity of the business. A focused single-GSTIN review of one financial year can often be completed in 3 to 4 weeks. A full-scope multi-GSTIN group review covering 3 to 5 years typically takes 6 to 10 weeks end-to-end, broken down roughly as: scoping and data room set-up (1 week), data review and walk-throughs (1 to 2 weeks), detailed testing across the check-point matrix (3 to 5 weeks), report drafting and client review (1 to 2 weeks). Remediation work — DRC-03 filings, amendments, credit notes, process redesign — runs in parallel or post-report. We scope the timeline explicitly in the engagement letter so that management expectations and board deliverables can be aligned upfront.
What are the most common issues uncovered in a GST Health Check?
While the mix varies by industry, the most recurring themes across our engagements include: ITC taken without matching GSTR-2B (Rule 36(4) and Section 16(2)(aa) breaches); incorrect or missed RCM liability on GTA, advocates, and security services under Section 9(3); blocked credits wrongly availed under Section 17(5) — typically on motor vehicles, food, construction, and employee-related expenses; common credit not reversed under Rule 42 / 43 where there are exempt outward supplies; missed cross-charge between distinct persons (branches with separate GSTINs) under Schedule I; credit notes issued beyond the November 30 cut-off under Section 34(2) leading to permanent loss of GST adjustment; exports not completed within 3 months under Rule 96A; and invoices issued without IRN where e-invoicing applied. Each of these can run into material quantums for mid-to-large taxpayers and is best detected and remediated voluntarily rather than via DRC-01.
How are findings of a Health Check remediated?
Remediation depends on the nature of the finding. Where a tax or ITC error is identified and the financial year is still open, correction flows through a subsequent GSTR-1 or GSTR-3B with interest under Section 50 where required. Where the period is closed or adjustment through returns is no longer feasible, voluntary payment via Form DRC-03 is typically the cleanest route — it creates a record of bona fide conduct and significantly reduces future penalty exposure. For documentation / process issues, remediation involves SOP redesign, contract amendments, ERP reconfiguration, and user training. For grey-area positions with real technical merit, we may recommend an Advance Ruling under Section 97 or a formal position paper with case-law support to be preserved as part of the audit trail. The report outlines a clear, prioritised remediation plan for each finding.
Does a GST Health Check protect against a departmental audit?
A Health Check does not prevent a Section 65 departmental audit from being ordered — the department has statutory powers under the CGST Act to conduct audits, and these are entirely outside the taxpayer's control. However, a Health Check materially changes the economics of any subsequent audit. By identifying and remediating issues in advance — filing amendments, reversing leaked ITC, paying DRC-03, and building a defence narrative — the taxpayer reduces the quantum of demand that the department can raise, strengthens the documentary record, and demonstrates bona fide conduct, which is often decisive in Section 74 fraud vs Section 73 non-fraud categorisation. Clients who undertake a Health Check before an ADT-01 typically face smaller adverse findings in ADT-02, lower penalty exposure, and cleaner adjudication outcomes.
How many years should a GST Health Check cover?
The optimal coverage period is dictated by limitation under Sections 73 and 74 of the CGST Act. Under Section 73 (non-fraud cases), the department can issue an SCN within 3 years from the due date of filing the annual return for the relevant financial year. Under Section 74 (fraud / suppression cases), the outer limit is 5 years. A Health Check therefore typically covers the last 3 financial years at minimum — and often 5 years for taxpayers in high-risk sectors or those with exposure to allegations of suppression. In M&A due diligence, coverage is aligned to the transaction-specific risk window and usually extends to all unassessed years. For ITC positions, coverage often needs to trace the full lifecycle of capital goods, which can stretch further back.
Can a GST Health Check be used in M&A due diligence?
Yes — in fact, GST due diligence in M&A transactions is essentially a Health Check executed against the commercial framework of the deal. On the buy-side, diligence identifies contingent GST liabilities (open notices, unassessed years, fraudulent credit risk), ITC at risk, refund pipeline exposure, and issues requiring specific indemnities or escrows in the definitive agreements. On the sell-side, a pre-emptive Health Check allows the seller to clean up issues before diligence begins, reducing price chips and representation / warranty exposure. For slump sale transactions, the review also covers whether the sale qualifies as "business as a going concern" exempt under Notification 12/2017-CT(R), and whether ITC-02 can be executed cleanly. A well-timed Health Check can materially affect deal valuation and structure.
What deliverables does the client receive from a GST Health Check?
The client receives a structured set of deliverables. First, an executive summary capturing the overall GST health, top five risks, and quantum of exposure. Second, an issue-wise detailed report — each issue described with factual background, applicable legal provision, finding, quantum estimate, risk rating (High / Medium / Low), and recommended corrective action. Third, supporting working papers — reconciliations, sample-testing results, evidence extracts, and case-law references. Fourth, a remediation roadmap with prioritised action items, owners, and target dates. Fifth, optional but highly valuable, an SOP pack for GST controls and a training session for the finance team. All deliverables are typically provided under confidentiality and, where engagement structure permits, with privilege / work-product protection considered.
Find Problems First. Fix Them On Your Terms.
Partner with our specialists for an end-to-end GST Health Check — 50+ check points, multi-year scope, risk-rated findings, and remediation support — delivered under one roof.
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