Since its inception, the Goods and Services Tax (GST) regime has been anchored on the principle of seamless flow of credit and digital compliance. The government’s gradual digitisation of compliance systems—GSTR-1/IFF for outward supplies, GSTR-2B for input tax credit, and GSTR-3B for payment of tax—has streamlined indirect tax administration considerably.

In October 2024, the Invoice Management System (IMS) was rolled out to enable recipients to view, accept, reject, or keep pending the invoices uploaded by suppliers. The tool empowered taxpayers to curate their input tax credit (ITC) directly on the GST portal rather than relying solely on auto-populated data.

Building upon this digital foundation, the Central Board of Indirect Taxes and Customs (CBIC) has now extended the IMS’s capability to cover import transactions through Bills of Entry (BoE). This enhancement marks a major stride towards integrating customs data with GST credit management.

New Addition: ‘Import of Goods’ Section in IMS

With effect from the October 2025 tax period, a new section titled “Import of Goods” has been introduced in IMS. Under this module, Bills of Entry filed for imports—including imports from Special Economic Zones (SEZs)—will now be visible to recipient taxpayers for review and confirmation.

Purpose and Functionality

Taxpayers will now be able to:

• View individual BoE records as transmitted from ICEGATE (Customs portal),

• Accept or keep such BoEs pending (rejection not permitted),

• Have the accepted BoEs reflected in their GSTR-2B automatically,

• Modify their actions until the filing of the corresponding GSTR-3B.

If no action is taken, the system will treat the BoE as deemed accepted. Draft GSTR-2B will continue to be generated on the 14th of the subsequent month.

This integration ensures that ITC on imports aligns seamlessly with the taxpayer’s self-assessment, thereby reducing mismatches and future disputes.

Structure of Import Data in IMS

The new section bifurcates import transactions into four sub-sections for clarity and traceability:

IMPG – Import of Goods from Overseas: For all original BoEs relating to imports from outside India.

IMPG (Amendments): For amendments in BoEs filed for overseas imports, covering both value and GSTIN amendments.

IMPGSEZ – Import of Goods from SEZ: For original BoEs related to procurement from SEZ units/developers.

IMPGSEZA (Amendments):For amended BoEs in SEZ-related imports, again covering value and GSTIN changes.

GSTIN Amendment Handling through IMS

A key addition in this advisory is the introduction of functionality to manage GSTIN changes in Bills of Entry—a frequent issue for multi-GSTIN entities or during business restructuring.

Current Challenge:

Earlier, when a BoE was filed with an incorrect GSTIN, and subsequently amended in Customs records, reconciling ITC between the original and amended GSTINs often required manual tracking and adjustment.

New Solution via IMS:

Under the new system:

• The previous GSTIN (G1) that initially claimed ITC must reverse such credit once a GSTIN amendment occurs.

• The amended GSTIN (G2) becomes eligible to claim ITC on the same BoE post-amendment.

• The IMS will automatically reflect reversal entries in blue for G1 under the IMPGA/IMPGSEZA categories.

• Taxpayers will have flexibility to declare partial or nil reversal amounts depending on whether ITC was already reversed earlier.

This structured workflow ensures that ITC is neither duplicated nor lost during transitions between GSTINs.

Illustrative Example

Suppose a company originally filed BoE No. 10123 in June 2025 under GSTIN G1. Later, due to a reorganisation, the GSTIN was amended to G2, followed by a value amendment in July 2025.

• The value amendment was already transmitted from ICEGATE and processed in GSTR-2B of G2.

• When the GSTIN amendment now reflects in IMS, only a reversal entry will appear for G1 (since G2 has already availed ITC).

This example illustrates the sophistication of the integration between ICEGATE, GSTN, and IMS in avoiding duplication of ITC.

Action Workflow for Import Bills of Entry

Taxpayers can take the following actions on each BoE record:

Rejection Not Permitted

The system explicitly disallows the “Reject” option for BoEs—presumably to prevent disputes since BoEs originate from Customs and not suppliers.

Restrictions on ‘Pending’

The “Pending” option cannot be exercised in cases such as:

• Downward value amendments where ITC has already been availed and 3B filed.

• ITC reversal entries linked to GSTIN amendments.

System Intelligence and Automatic Adjustments

Several automated controls have been built into the IMS:

Latest Amendments Supersede Old Ones: Where multiple amendments exist, only the latest version of the BoE will be visible in IMS.

Conditional Removal of BoEs from IMS: When a GSTIN amendment occurs before GSTR-3B filing by G1, the original BoE disappears from G1’s dashboard. If multiple amendments exist, earlier records are replaced automatically.

Recomputation Requirement: Any post-14th changes in action (accept/pending) require recomputation of GSTR-2B from the IMS dashboard before filing GSTR-3B.

Persistence of Pending Records: Pending BoEs will continue to appear in subsequent tax periods until acted upon, ensuring no record is lost.

Impact on GSTR-2B and GSTR-2A Formats

The integration brings structural changes to both the GSTR-2B and GSTR-2A formats for greater transparency.

Changes in GSTR-2B:

• New columns added for:

  • Type of Amendment (Value/GSTIN)

  • ITC reduction requirement (Yes/No)

  • Amount declared for ITC reduction – IGST and Cess.

• The previous “Amended (Yes/No)” column has been removed.

• Separate worksheets will now exist for each category: IMPG, IMPGA, IMPGSEZ, and IMPGSEZA.

Changes in GSTR-2A:

• A new “Type of Amendment” column added under Amendment History.

• Original and amended GSTIN records will now be traceable through linked entries, maintaining complete audit trails for both versions.

Compliance Implications for Businesses

The advisory’s implications are far-reaching for importers and multi-GSTIN entities. Key takeaways include:

Enhanced Visibility of Imports: Taxpayers can now verify import ITC directly within IMS instead of reconciling manually using ICEGATE data, thereby minimising mismatches.

Automated Credit Flow for GSTIN Amendments: Credit reversal and reallocation between old and new GSTINs will now be system-driven, reducing manual interventions and human error.

Mandatory Review for Accurate ITC Claims: As deemed acceptance applies to inaction, taxpayers must institutionalise review processes to prevent inadvertent acceptance of ineligible credits.

Revised Reconciliation Timelines: With GSTR-2B draft generation fixed at the 14th of the next month, internal teams must complete their import data verification before this date.

Documentation Control: The four-category segregation (IMPG/IMPGSEZ and their amendment counterparts) will necessitate more structured documentation for audits.

Audit Trail Strengthening: GSTR-2A’s new amendment history feature will make it easier for tax authorities to track the life cycle of each BoE—reducing ambiguity during scrutiny.

Procedural Changes for Accountants and CFOs

For CFOs, Controllers, and GST managers, the following operational adjustments are advised:

Internal SOPs for IMS Review: Develop month-end standard operating procedures for reviewing and acting upon BoEs in IMS, especially focusing on high-value imports.

Cross-Department Coordination: Ensure coordination between logistics, customs, and tax teams so that BoE amendments or GSTIN changes are reflected promptly in IMS.

Reconciliation with ICEGATE: Although IMS will now mirror ICEGATE data, a monthly cross-verification is still essential to detect transmission delays or mismatches.

System Update Training: Account teams should be trained to navigate the new IMS interface and understand the implications of each action type (Accept/Pending).

GSTR-2B Recomputation: Reinforce the importance of recomputing GSTR-2B whenever any action is modified post the 14th of the subsequent month.

Strategic Implications: Moving Toward Full Digital Synchronisation

This move by the GSTN and CBIC is not merely procedural—it reflects the broader vision of creating a digitally unified tax ecosystem. By embedding import data directly into IMS, the system effectively eliminates the silo between GST compliance and customs compliance.

Such integration will also pave the way for:

• AI-based credit validation, using Customs and GSTN data cross-references,

• Real-time mismatch alerts, and

• Reduced litigation relating to import ITC eligibility.

Conclusion: A Step Towards Seamless ITC Governance

The introduction of the Import of Goods functionality in IMS is a landmark step in aligning India’s indirect tax and customs ecosystems. It represents the maturing of GST’s digital infrastructure—offering transparency, traceability, and accountability at every stage of the import ITC lifecycle.

While the system automates much of the complexity, businesses must remain vigilant in:

• Periodic verification of BoE data,

• Timely reversal of ITC under GSTIN amendments, and

• Ensuring all accepted records are based on valid imports and correctly classified entries.

For organisations managing multiple GSTINs, this advisory offers both convenience and compliance discipline. However, as the onus of self-assessment continues, robust internal governance will remain key to avoiding ITC disputes.

Frequently Asked Questions – GST Reforms 2.0