GSTN Advisory on Import of Goods in Invoice Management System (IMS) - Dated 30th October 2025

By

Dr. Muhammed Mustafa C T
Senior Tax Consultant & Managing Director, BRQ Associates
"Educating India for Better Tax Compliance"

Introduction

The Invoice Management System (IMS), introduced on the GST portal from October 2024, marked a major milestone in improving Input Tax Credit (ITC) accuracy and reconciliation. The system allowed taxpayers to accept, reject, or keep pending invoices uploaded by suppliers through GSTR-1, GSTR-1A, or IFF.

To further enhance compliance and ease of doing business, GSTN has now introduced a new section - “Import of Goods” - within IMS. This functionality becomes effective from the October 2025 tax period and will integrate Bills of Entry (BoE) filed for imports (including from SEZs) directly into the IMS interface

Purpose and Functionality

This enhancement enables taxpayers to:

• View all their import-related BoEs directly in IMS.
• Take suitable actions like Accept or Keep Pending for each Bill of Entry.
• Understand that no action taken will be considered as “Deemed Accepted” by the GST system.
• Auto-generate draft GSTR-2B on the 14th of the subsequent month based on actions taken.

Importantly, taxpayers can still modify these actions before filing the corresponding GSTR-3B

Sub-Sections in Import of Goods (IMS)

According to the advisory (Page 1), the IMS now includes four key categories:

1. IMPG - Import of Goods from Overseas:
   For all original BoEs filed for import of goods from outside India.
2. IMPG (Amendments):
   For value or GSTIN amendments made to those BoEs.
3. IMPGSEZ - Import of Goods from SEZ:
   For all original BoEs filed for imports from Special Economic Zones.
4. IMPGSEZA (Amendments):
   For amendments made to SEZ import BoEs, including value and GSTIN changes.

Handling GSTIN Change in Bill of Entry (BoE)

Where the GSTIN linked to a Bill of Entry is later amended, complex ITC implications arise. The advisory (Page 2) clearly states that:

• If the previous GSTIN (G1) already availed ITC on that BoE, it must reverse the credit.
• IMS now automates this - showing ITC reversal entries under the “Amendment Type: GSTIN.”

• The previous GSTIN can indicate:
  • Zero value - if ITC already reversed earlier.
  • Partial value - if ITC partly reversed earlier.
  • Full reversal - if ITC entirely needs to be reversed.

The corresponding ITC is then made available to the new GSTIN (G2) in its GSTR-2B after adjustment

Illustration

Example:
A taxpayer imported goods under BoE No. 10123 using GSTIN “G1” in June 2025 and later changed to “G2.”
A value amendment occurred in July 2025.
Here, ITC already flowed to G2 due to value amendment, so the reversal entry will only appear in G1.
No further ITC entry will be shown to G2 to avoid duplication.

Actions Allowed on Bills of Entry (BoE)

As per the advisory (Page 3), taxpayers can perform three actions:

1. Accept:
   Confirms that the import is correct and eligible for ITC. The record becomes part of “ITC Available” in GSTR-2B and auto-populates in GSTR-3B.
2. Pending:
   Defers the claim of ITC. Such BoEs will remain in IMS but not flow to GSTR-2B/3B.
3. No Action Taken:
   Treated as Deemed Accepted while generating GSTR-2B.

“Reject” is not allowed for BoEs.

Restrictions on “Pending” Action

Taxpayers cannot mark BoEs as Pending in these cases:

• When there’s a downward value amendment after ITC is already availed in GSTR-3B.
• For reversal of ITC due to GSTIN amendment in the previous GSTIN.

Only the latest amendment record will remain visible in IMS in case of multiple amendments

Other Key Functionalities

As per pages 4-5 of the advisory:

1. Partial Save Restrictions:
   IMS will not save “Pending” actions in cases of downward amendments or ITC reversals until the taxpayer first takes action on the original record.
2. Automatic Removal from Dashboard:
   • When GSTIN amendments occur before filing GSTR-3B, original BoE disappears from G1’s dashboard.
   • Only the latest amended BoE remains visible when multiple amendments exist.
3. Mandatory Re-computation:
   Any change in action after 14th of the next month requires recomputing GSTR-2B.
4. New Columns in GSTR-2B:
   • Type of Amendment
   • ITC reduction required (Yes/No)
   • ITC reduction (IGST / Cess amounts)
5. GSTR-2A Updates:
   • “Type of Amendment” column added in Amendment History.
   • Both the previous and amended GSTINs will show records appropriately.

Practical Impact on Taxpayers

• Enhanced ITC accuracy: Imports are now integrated within IMS, reducing manual reconciliation.
• Deemed acceptance principle: Ensures timely processing and discourages non-compliance.
• Streamlined amendment handling: Both value and GSTIN amendments are traceable across GSTINs.
• SEZ Imports visibility: Import from SEZs treated similar to foreign imports under distinct sub-sections.

Advisory for Tax Consultants and Businesses

1. Regularly monitor IMS dashboard to avoid “deemed acceptance” of incorrect BoEs.
2. Review GSTIN amendments to ensure ITC reversal and re-availment are properly reflected.
3. Recompute GSTR-2B before filing GSTR-3B whenever any BoE status changes.
4. Maintain import reconciliation reports between ICEGATE and IMS for audit preparedness.
5. Educate import-heavy clients (especially SEZ and EOU units) about new compliance checkpoints.

Legal References

• Section 16 & 17, CGST Act, 2017 - Conditions and restrictions for availing ITC.
• Rule 36, CGST Rules, 2017 - Document-based ITC conditions (BoE is a valid document).
• Section 37 & 38, CGST Act - Outward and inward supply details.
• Section 42 & 43A (proposed) - Matching, reversal, and reclaim of ITC.
• Circular No. 183/15/2022-GST - ITC matching principles and GSTR-2B utility.

Conclusion

The introduction of “Import of Goods” in IMS marks another significant step in India’s digital GST compliance evolution.
By linking customs data (BoE) directly with GST returns, this reform enhances transparency, ensures correct ITC flow, and reduces disputes.

Taxpayers must proactively review and act on their Bills of Entry within IMS to safeguard their Input Tax Credit and maintain seamless compliance.

Author:
Dr. Muhammed Mustafa C T
Senior Tax Consultant & Managing Director, BRQ Associates
"Educating India for Better Tax Compliance."