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GST|April 202618 min readChecklist

GST Annual Return FY 2025–26: A Readiness Checklist

Tables to reconcile, IMS-driven ITC auto-population, and the form-level changes you need to plan for before filing GSTR-9 and GSTR-9C for FY 2025–26.

Key takeaways

GSTR-9 for FY 2025–26 is due by 31 December 2026. GSTR-9 remains optional for taxpayers with aggregate turnover up to ₹2 crore (continuing the relief granted via Notification 15/2025-Central Tax for FY 2024–25).

GSTR-9C self-certified reconciliation is mandatory once aggregate turnover crosses ₹5 crore. There is no statutory CA/CMA audit requirement — the certification is the registered person's own.

Table 8A is now driven by the Invoice Management System (IMS): auto-population pulls invoices accepted (or deemed accepted) in IMS that appear in GSTR-2B, sourced by document date. Build an IMS-action SOP during the year, not in November.

Table 6A1 — introduced via Notification 16/2025-Central Tax — separately captures ITC of the preceding FY claimed in the current FY. Maintain a clean cross-year ledger to populate this without rework.

Late fee under Section 47 is ₹50/day for turnover up to ₹5 cr; ₹100/day for ₹5–20 cr; and ₹200/day above ₹20 cr (each split equally between CGST and SGST), capped per Notification 7/2023-Central Tax.

What 'Annual Return' Means in FY 2025–26 Due Dates, Late Fees, and the Cost of Slippage Structural Changes Carried into FY 2025–26 GSTR-9 Tables: A Reconciliation-First Walkthrough Common Errors and How to Pre-empt Them Your FY 2025–26 GSTR-9/9C Readiness Checklist

01What 'Annual Return' Means in FY 2025–26

The GST annual return is not a single form but a stack: GSTR-9 (the return), GSTR-9C (the self-certified reconciliation), and the underlying workpapers that bridge books, the GSTN portal, and the IMS-driven ITC ledger. Each layer has its own threshold, its own due date logic, and its own evidentiary purpose.

FY 2025–26 carries forward the structural changes notified for FY 2024–25 — most importantly the IMS auto-population in Table 8A, the cross-year ITC capture in Table 6A1, and the e-commerce supplies disclosure under Section 9(5) in GSTR-9C. Treat these as the new baseline rather than one-off changes.

Annual return obligations by aggregate turnover

PAN-level aggregate turnover	GSTR-9	GSTR-9C
Up to ₹2 crore	Optional (waived)	Not required
₹2 crore to ₹5 crore	Mandatory	Not required
Above ₹5 crore	Mandatory	Mandatory (self-certified)

Aggregate turnover — the right denominator

Aggregate turnover is computed at PAN level across all GSTINs and includes taxable, exempt, export, and inter-state supplies (excluding inward supplies under reverse charge and CGST/SGST/IGST/cess). A ₹4.8 crore GSTIN inside a ₹5.6 crore PAN-level entity still triggers GSTR-9C.

Composition taxpayers do not file GSTR-9 — they file GSTR-9A (currently waived) and the quarterly statement GSTR-4 (annual since FY 2019–20). E-commerce operators collecting TCS file GSTR-9B. Casual taxable persons, non-resident taxable persons, ISDs, and TDS deductors are exempt from GSTR-9.

02Due Dates, Late Fees, and the Cost of Slippage

The statutory due date for GSTR-9 (and GSTR-9C, where applicable) is 31 December immediately following the end of the financial year. For FY 2025–26 that means a 31 December 2026 deadline. CBIC has historically issued targeted extensions when portal issues arise; assume the statutory date holds and treat any extension as a bonus.

Late fee under Section 47(2) of the CGST Act

From FY 2022–23 onwards, the late fee for GSTR-9 was rationalised by Notification 07/2023-Central Tax dated 31 March 2023 into three turnover-based slabs:

GSTR-9 late fee slabs (CGST + SGST combined)

Aggregate turnover	Per-day late fee	Maximum cap
Up to ₹5 crore	₹50 (₹25 CGST + ₹25 SGST)	0.04% of turnover in State/UT (0.02% per Act)
₹5 crore to ₹20 crore	₹100 (₹50 CGST + ₹50 SGST)	0.04% of turnover in State/UT (0.02% per Act)
Above ₹20 crore	₹200 (₹100 CGST + ₹100 SGST)	0.50% of turnover in State/UT (0.25% per Act)

Late fee for GSTR-9C is governed by the same Section 47 framework — ₹200 per day capped at 0.50% of turnover under the State/UT GST law. The cap is per registration, so a single PAN with multi-state registrations multiplies the exposure quickly.

Notice exposure beyond the late fee

Delay in filing GSTR-9 also slows ITC validation and tax officer scrutiny. Notices under Sections 73/74 typically reference reconciliation gaps that GSTR-9 should have resolved. Filing late often means responding to notices on the same data twice.

03Structural Changes Carried into FY 2025–26

Three notifications redrew the FY 2024–25 GSTR-9/9C: Notification 13/2025-Central Tax (CGST Rules amendments and reporting fields), Notification 15/2025-Central Tax (₹2 crore exemption continued), and Notification 16/2025-Central Tax (GSTR-9 format updated for IMS-based auto-population and new reversal disclosures). Until further notified, these flow into the FY 2025–26 cycle.

Table 8A is now IMS-driven

–Auto-population in Table 8A pulls invoices by document date, not by reporting period — so an FY 2025–26 invoice that appears in GSTR-2B of FY 2026–27 (because the supplier filed late) still appears in your FY 2025–26 Table 8A.

–The pull happens only for documents accepted or deemed accepted in IMS. Pending or rejected invoices do not flow.

–IMS actions do not create new ITC eligibility — they govern what shows up in 2B and, in turn, in Table 8A. The substantive eligibility test under Section 16 still applies.

Table 6A1 — cross-year ITC

The new Table 6A1 captures ITC pertaining to the preceding FY that has been claimed in the current FY — the typical April–October window of the year following supply. Maintain a separate ledger of (a) supplier GSTIN, (b) invoice date, (c) invoice value, (d) ITC amount, and (e) the GSTR-3B period in which it was claimed. This is the workpaper that defends the Table 6A1 figure.

GSTR-9C reconciliation reframed

–E-commerce Section 9(5) supplies (food delivery, ride-share, etc.) now have a separate disclosure field so they are not merged with regular B2C sales of the operator.

–Reconciliation is computed against tax payable rather than tax paid — unpaid liabilities surface explicitly rather than being absorbed into 'differences'.

–Additional liability identified during reconciliation can be discharged in cash or through available ITC, removing a frequent practical bottleneck.

04GSTR-9 Tables: A Reconciliation-First Walkthrough

GSTR-9 is organised into six parts and 19 tables. Use this map to plan workpapers — not every table needs the same depth.

GSTR-9 — part and table summary

Part	Tables	What it covers
Part I	1–3	Basic details and turnover
Part II	4–5	Outward supplies — taxable (Table 4) and non-taxable (Table 5)
Part III	6–8	ITC — availed (6), reversed/ineligible (7), reconciliation with 2B (8)
Part IV	9	Tax paid as declared in returns
Part V	10–14	Transactions for the FY declared in returns of the next FY (April–October)
Part VI	15–19	Demands, refunds, supplies from composition dealers, HSN-wise supplies, late fees

Tables 4 and 5 — outward supplies

–Table 4 captures taxable outward supplies. Reconcile with the sum of Table 3.1(a)/(b)/(c) of GSTR-3B and the supply-side rows of GSTR-1/IFF for the year, including amendments through October of the next FY.

–Table 5 captures outward supplies on which tax is not payable — zero-rated supplies, exempt supplies, nil-rated, and non-GST supplies. Make sure exports without payment of tax (LUT) sit in 5A, not 4C.

–Reverse charge supplies (where the recipient pays tax) sit in Table 4G — not in Table 5.

Tables 6, 7, and 8 — the ITC trio

–Table 6 is the gross ITC availed. Sub-rows capture inward supplies other than RCM/imports (6B), inward RCM from unregistered (6C) and registered (6D) persons, import of goods (6E) and services (6F), ISD credit (6G), and reclaimed ITC (6H).

–Table 7 is reversals — Rules 37, 37A, 38, 42, 43; ineligible ITC under Section 17(5); TRAN-1 (7F) and TRAN-2 (7G). Taxpayers can use 7A–7E or consolidate into 7H, but 7F and 7G are mandatory if applicable.

–Table 8 is the reconciliation — ITC as per GSTR-2B (8A, now IMS-driven), ITC availed in 3B (8B), ITC of FY availed in next FY's GSTR-3B (8C), and the difference (8D). Table 8 does not affect liability — its role is to surface mismatches.

Single working paper for ITC

Build one master ITC workpaper for the year that flows: GSTR-2B (raw) → IMS actions → books → GSTR-3B claimed → reversals → net availed. This single sheet feeds Tables 6, 7, 8, 12, and 13 with audit-ready references.

Tables 12 and 13 — prior-year corrections

Table 12 captures ITC of the FY reversed in returns of the next FY (up to the prescribed date). Table 13 captures ITC of the FY availed in returns of the next FY. Together with Table 6A1 (introduced under Notification 16/2025), these tables tell the cross-year story — keep the underlying register reconciled monthly.

05Common Errors and How to Pre-empt Them

01Treating Table 8A as gospel. IMS-driven 8A only includes accepted/deemed-accepted invoices. Compare 8A against your books — a missing supplier invoice in IMS is still an eligibility issue you must resolve.

02Misclassifying Section 9(5) supplies. E-commerce operators handling food delivery or ride-share must report these distinctly in GSTR-9C; merging with regular B2C creates reconciliation gaps that snowball into notices.

03Skipping Table 6A1 for cross-year ITC. Claims of FY 2024–25 ITC in FY 2025–26 GSTR-3B (April–October 2026) must populate Table 6A1 of the FY 2025–26 return. Skipping this shifts the mismatch into Table 8 and looks like an unexplained gap.

04Ignoring RCM under-reporting. Reverse charge inward supplies missed in monthly 3B but identified during the year-end review must be paid in cash with interest under Section 50, then disclosed in Table 6C/6D.

05Computing late fee on a single GSTIN basis. The cap operates per registration. A PAN with five state registrations sees five separate caps — do not assume a single cap covers all GSTINs.

06Filing GSTR-9 before reconciling GSTR-1 vs GSTR-3B. Differences here are the most common audit query. Resolve them in the period filings (or DRC-03) before the annual return locks the numbers.

DRC-03 is your only correction path post-filing

GSTR-9 cannot be revised once filed. Any additional liability discovered later must be paid via DRC-03. If interest under Section 50 applies, it runs from the original due date of the GSTR-3B in which the liability should have been declared — not from the GSTR-9 filing date.

06Your FY 2025–26 GSTR-9/9C Readiness Checklist

Books-to-portal reconciliation pack

01Reconcile turnover per books (audited financials) with the sum of GSTR-1/IFF for the year, including amendments through GSTR-1 of October 2026.

02Reconcile output tax per books with Table 3.1 of GSTR-3B for the year; map each variance to a specific invoice or amendment.

03Build a complete IMS log: total invoices received, accepted, rejected, kept pending. Track aging on pending invoices — they are blocking ITC.

04Pull GSTR-2B (consolidated) and reconcile against (a) ITC books and (b) ITC claimed in GSTR-3B. Document each gap with a 'why' note (supplier not filed, IMS pending, ineligible under Section 17(5), etc.).

05Maintain a separate cross-year ITC register: FY 2024–25 ITC claimed in FY 2025–26 (Table 6A1) and FY 2025–26 ITC expected in FY 2026–27 (informs Table 13 next year).

06List every RCM transaction — imports, services from unregistered, GTA, legal, sponsorship, security — reconcile cash-paid liability with ITC availed.

GSTR-9C self-certification pack

01Map turnover from audited financials to GSTR-9 turnover; explain every reconciling item with a workpaper reference.

02Reconcile tax payable per books with tax payable per GSTR-9; document any DRC-03 already paid during the year.

03Capture Section 9(5) e-commerce supplies separately; do not merge with regular B2C.

04Confirm ITC reconciliation between books and GSTR-9 Table 6/7/8 sums.

05Prepare a one-page self-certification note covering scope, methodology, and key judgements.

Governance and timing

–Lock final period-end position by 30 September 2026 to leave a clean buffer for the October 2026 GSTR-1/3B amendments and the ITC cut-off.

–Run a dry-run GSTR-9 by 30 November 2026; share with management and statutory auditors.

–File GSTR-9 (and GSTR-9C, where applicable) by 15 December 2026 to avoid portal congestion and last-minute surprises.

–Keep a workpaper bundle indexed against each GSTR-9 table for at least six years, in line with Section 36 record retention requirements.

Two-pass review

Have one team build the workpapers and a second reviewer go top-down: turnover, ITC, RCM, exports/SEZ, e-commerce. Independent review catches misclassifications that the preparer's working paper hides in plain sight.

CA Siddharth A Shah

CA Siddharth A Shah & Associates, Vadodara

This article is for informational purposes only and does not constitute professional advice. Tax laws are subject to change. Readers should consult a qualified Chartered Accountant for advice specific to their situation. Published April 2026.

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