GST IMS Compliance for June 2026 Filing: A Practical Guide

The Invoice Management System (IMS) has been live since October 2024, but the April 2026 amendments — which hardwired IMS action status directly into the ITC availability logic under Sec 16(2)(c) of the CGST Act — have fundamentally changed your month-end close. If your GSTR-3B auto-populated figures do not match your books this June, the IMS action queue is almost certainly the reason. Here is the practical workflow to fix it before the filing deadline.

What Changed in April 2026 and Why It Affects June ITC

From 1 April 2026, an invoice that sits in your IMS dashboard in a "Pending" state at the time you file GSTR-3B is treated as if you have not accepted it. The system will not flow that ITC into Table 4(A) of your return. This is the operational consequence of the CBIC clarification issued under Rule 37A of the CGST Rules — suppliers who have filed GSTR-1 but whose invoices you have not actioned in IMS will block your credit for that tax period.

Previously, a passive taxpayer could ignore IMS and still claim credit through GSTR-2B auto-population. That safety net is gone. Every invoice in your IMS queue now demands an explicit decision — Accept, Reject, or Pending (defer) — and that decision has direct cash-flow consequences.

Check the official CBIC portal at cbic-gst.gov.in for the latest notifications and circulars governing IMS workflow, as the system continues to receive incremental updates.

The Three-Tier IMS Action Logic You Must Understand

Before you touch the reconciliation, internalise how the system classifies invoices:

IMS Status	Effect on GSTR-2B	ITC in GSTR-3B Table 4(A)
Accepted	Included in current month GSTR-2B	Available for claim
Rejected	Removed from GSTR-2B; supplier's GSTR-1 flagged	Not available; supplier must issue credit note
Pending	Deferred to next month's GSTR-2B cycle	Blocked in current month; flows next month if accepted
No Action taken	Treated as Pending from April 2026	Blocked — this is the most common June 2026 problem

The "No Action = Pending" rule is where most firms are losing ITC right now. A vendor uploads an invoice of ₹5,00,000 + ₹90,000 GST (18%). If your team has not actioned it in IMS, your GSTR-3B will show ₹90,000 less ITC than your purchase register — triggering a reversal entry or, worse, a cash outflow via increased tax payable.

Step-by-Step IMS Reconciliation for June 2026

Work through this sequence before you open the GSTR-3B filing screen.

Step 1 — Pull the IMS Dashboard Report Log in to the GST portal, navigate to Services → Returns → Invoice Management System, and download the IMS action report for the May 2026 invoice period (the source period for your June 2026 GSTR-3B). Export it as Excel. You need three columns: Supplier GSTIN, Invoice Number, and Current Status.

Step 2 — Match Against Your Purchase Register In Tally Prime or Zoho Books, run a purchase register for May 2026. Cross-reference every inward supply entry against the IMS export. Any purchase register line without a matching "Accepted" status in IMS is a blocked credit item. Flag these immediately.

Step 3 — Categorise the Exceptions Your exceptions will fall into four buckets:

• Supplier has not filed GSTR-1 — invoice will not appear in IMS at all; ITC is unavailable under Sec 16(2)(c) until supplier files.
• Invoice in IMS but status = No Action/Pending — action it before GSTR-3B filing cutoff.
• Invoice amount or tax mismatch — reject in IMS, raise a debit note query with the supplier.
• Invoice belongs to prior period — check if it has appeared in a previous GSTR-2B; do not double-claim.

Step 4 — Action All Pending Invoices For every invoice where the amount in your books matches the IMS record exactly, click Accept in bulk using the IMS batch action tool. Do this at least 48 hours before filing — the portal takes time to regenerate the GSTR-2B delta after bulk actions.

Step 5 — Recompute Table 4(A) of GSTR-3B After actions are complete, refresh your GSTR-3B draft. Table 4(A)(5) — "All other ITC" — should now reflect the updated GSTR-2B figure. Cross-check this against your IMS-reconciled purchase register. Any residual difference must be explained and documented before filing.

Handling the Blocked ITC Scenarios

Scenario A: Supplier has filed GSTR-1 late — invoice arrives mid-month If a supplier files GSTR-1 for May on 14 June 2026 (within the extended due date), the invoice will appear in your IMS queue before the 20 June GSTR-3B deadline. You have a narrow window to accept it. Assign someone to monitor IMS daily in the second week of each month specifically for this purpose.

Scenario B: Invoice value in IMS differs from your books Example: Your books show ₹2,50,000 taxable value; IMS shows ₹2,30,000. Do not accept blindly. Reject the invoice in IMS, communicate the discrepancy to the supplier, and request a corrected invoice or credit note. Claiming ITC on an incorrect value creates a reconciliation gap that will surface in GSTR-9 and trigger a notice under Sec 61 scrutiny.

Scenario C: Supplier is on the cancelled GSTIN list If the supplier's GSTIN was cancelled before the invoice date, the invoice should not appear in IMS. If it somehow does, reject it and escalate — ITC on an invoice from a cancelled GSTIN is ineligible under Rule 36(1) of CGST Rules.

Scenario D: B2B invoice uploaded under wrong category by supplier Suppliers sometimes upload a B2B invoice as B2BA (amended) or vice versa. This causes a duplicate or missed entry in IMS. Contact the supplier to file an amendment in their GSTR-1, then re-action the corrected entry in your IMS queue.

Month-End IMS Checklist for June 2026 Filing

Use this checklist for every regular taxpayer entity you manage:

• Download IMS action report by 10th of the filing month
• Reconcile IMS report against purchase register — flag all non-"Accepted" lines
• Confirm all major suppliers (top 20 by invoice value) have filed GSTR-1
• Batch-accept all verified, amount-matched invoices by 13th of the month
• Reject all mismatched invoices and notify suppliers in writing
• Check for any GSTR-1A amendments filed by suppliers that override earlier entries in IMS
• Revalidate GSTR-2B post-actions and reconcile to within ₹500 tolerance
• Document residual differences with reason codes before filing
• File GSTR-3B only after sign-off on the reconciliation working paper
• Archive the IMS export, reconciliation workbook, and GSTR-2B PDF for audit trail

For firms handling multiple GSTINs, this checklist should be a shared tracker — not a mental note. One missed "Accept" on a ₹10 lakh invoice means ₹1.8 lakh in blocked ITC (at 18% GST), which has to be either carried forward or paid from working capital.

Common IMS Portal Errors and How to Fix Them

Error: "GSTR-2B not generated" — This occurs when a supplier has filed GSTR-1 but the portal has not yet processed the delta into your GSTR-2B. Wait 24 hours after the supplier confirms filing, then refresh IMS. If the issue persists beyond 48 hours, raise a grievance on the GST portal under Help → Raise Grievance.

Error: "Invoice already actioned in previous period" — The system is flagging a duplicate. Check whether the invoice number appeared in a prior month's GSTR-2B. If so, do not re-action; the ITC was already eligible in the earlier period.

Error: "Supplier GSTIN inactive" — Verify the supplier's registration status on cbic-gst.gov.in before proceeding. Do not accept invoices from inactive GSTINs.

Error: "Bulk action failed for X invoices" — Usually a portal timeout. Reduce batch size to 50 invoices at a time and retry. If the error persists, action individually and screenshot each confirmation.

Building an IMS-Ready Practice for the Rest of FY 2026-27

The June 2026 filing is a stress test, but the underlying discipline needs to be permanent. Build the IMS reconciliation into your monthly engagement calendar as a fixed deliverable — not a firefighting task on the 19th. Firms that are doing this well have already integrated IMS status into their purchase approval workflows, so a supplier's GSTR-1 filing status is verified before payment release, not after.

If your team is still reconciling manually in Excel, consider building a semi-automated matching template — GSTIN + Invoice Number as the composite key — that pulls from both the IMS export and your ERP's purchase register. The matching logic is straightforward, and two hours of setup now saves five hours of panic at month-end.

Want to benchmark your IMS workflow against peers and identify gaps? The SuperAccountant practice quiz covers IMS, GSTR reconciliation, and ITC eligibility — take it at https://app.superaccountant.in/en/quiz.

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