GST WEEKLY UPDATE :12/2025-26 (22.06.2025) By CA Vipul Khandhar

-By Vipul Khandhar

1. Introduction of Enhanced Inter-operable Services Between E-Way Bill Portals:

GSTN is pleased to inform that NIC shall be launching the new E-Way Bill 2.0 portal (https://ewaybill2.gst.gov.in) on 1st July 2025, featuring enhanced inter-operable E-Way Bill functionalities. The portal is being introduced to provide enhanced inter-operability between the existing E-Way Bill 1.0 Portal (https://ewaybillgst.gov.in) and the new portal.

1. Objective
   The new E-Way Bill 2.0 portal has been developed in response to taxpayers’ demands for continuity in services during exigencies. It enables cross-portal access to critical E-Way Bill functionalities, ensuring seamless operations for taxpayers and transporters. 

2. New Inter-Operable Services

The following additional services will be available on the E-Way Bill 2.0 portal for E-Way Bills generated on either portal (E-Way Bill 1.0 or E-Way Bill 2.0):

1. a) Generation of E-Way Bill based on Part-A details entered by the supplier
2. b) Generation of Consolidated E-Way Bills
3. c) Extension of validity of E-Way Bills
4. d) Update of transporter details
5. e) Retrieval of consolidated E-Way Bills

These services are in addition to the currently available cross-functional services:

1. a) Generation of E-Way Bills
2. b) Updating of vehicle details
3. c) Printing of E-Way Bills 

3. System Integration and Synchronization

a) Both portals will operate on a real-time synchronized architecture wherein E-Way Bill data will be mirrored across both systems within seconds

b) In the event of a technical issue or downtime on the E-Way Bill 1.0 portal, taxpayers may perform all necessary operations (e.g., updating Part-B) on the E-Way Bill 2.0 portal and carry the E-Way Bill slip generated therefrom.

c) This dual-system approach is designed to eliminate dependency on a single portal and ensure business continuity.

4. Availability via API

All the above services will also be made available to taxpayers and logistics operators through APIs, in addition to the web portal interface. These APIs are currently hosted on the sandbox environment for testing and integration purposes. 

5. Key Benefits

Eventually, the data from both E-Way Bill1 and E-Way Bill2 portals shall be seamlessly merged and integrated, thereby eliminating dependency on the E-Way Bill1 system during exigencies. The E-Way Bill2 portal is designed to synchronize E-Way Bill details with the main portal within a few seconds.

Criss-cross operations between the two portals are fully enabled — updates made to E-Way Bills generated on the E-Way Bill1 portal can be carried out on the E-Way Bill2 portal, and vice versa. In the event of non-availability of the main portal due to technical reasons, Part-B details of E-Way Bills generated on the E-Way Bill1 portal can be updated through the E-Way Bill2 portal, and both versions of the E-Way Bill slip may be carried accordingly.

Taxpayers and logistics operators are encouraged to familiarize themselves with the new functionalities and integrate API services where applicable.

2. Advisory to file pending returns before expiry of three years:

As per the Finance Act,2023 (8 of 2023), dt. 31-03-2023, implemented w.e.f 01-10-2023 vide Notification No. 28/2023 – Central Tax dated 31th July, 2023, the taxpayers shall not be allowed file their GST returns after the expiry of a period of three years from the due date of furnishing the said return under Section 37 ( Outward Supply), Section 39 (payment of liability), Section 44 ( Annual Return) and Section 52 (Tax Collected at Source). These Sections cover GSTR-1, GSR-1A, GSTR 3B, GSTR-4, GSTR-5, GSTR-5A, GSTR-6, GSTR 7, GSTR 8 and GSTR 9 or 9C.

Hence, above mentioned returns will be barred for filing after expiry of three years. The said restriction will be implemented on the GST portal from July 2025 Tax period. Which means any return for which due date was three years back or more and hasn’t been filed till July Tax period will be barred from Filling. In this regard an advisory was already issued by GSTN on October 29th, 2024

Illustration : For ease of reference and better clarity, the latest GST returns that will be barred from filing w.e.f 1st August 2025 are detailed in the table below:

Hence, the taxpayers are once again advised to reconcile their records and file their GST Returns as soon as possible if not filed till now.

3. Handling of Inadvertently Rejected records on IMS:

Question 1: How can a recipient avail ITC of wrongly rejected Invoices/ Debit notes/ECO-Documents in IMS as corresponding GSTR-3B of same tax period was also filed by recipient?

Answer: In such cases recipient can request to the corresponding supplier to report the same record (without any change) in same return period’s GSTR-1A or respective amendment table of subsequent GSTR-1/IFF. Thus, recipient can avail the ITC basis on amended record by accepting such record on IMS and recomputing GSTR-2B on IMS. Here the recipient will get ITC of complete amended value as original record was rejected by the recipient.

However, recipient will be able to take ITC for the again furnished document by the supplier, as stated above, only in the GSTR-2B of the concerned tax-period.

Question 2: If any original record is rejected by the recipient and supplier furnishes the same record in GSTR-1A of same tax period or in the amendment table of GSTR-1/IFF of subsequent period, till the specified time limit, then what impact it will have on supplier’s liability?

Answer: In case supplier had furnished an original record in GSTR-1/IFF but the same record was rejected wrongly by the recipient in IMS. In such cases supplier on noticing the same in the supplier’s view of IMS dashboard or on request of recipient, may furnish the same record again (without any change) in GSTR-1A of same tax period or in the amendment table of GSTR-1/IFF in any subsequent period, till the specified time limit, then the liability of supplier will not increase. As amendment table take delta value only. Thus, in present case of same values, differential liability increase will be zero.

Question 3: As a recipient taxpayer, how to reverse ITC of wrongly rejected Credit note in IMS as the corresponding GSTR-3B has already been filed?

Answer: In such cases recipient can request the concerned supplier to furnish the same Credit note (CN) without any change in the same return period’s GSTR-1A or in amendment table of subsequent period’s GSTR-1/IFF. Now recipient can reverse the availed ITC based on the amended CN by accepting the CN on IMS. Hence, the recipient’s ITC will get reduced with complete amended value, as soon as the recipient recomputes GSTR-2B on IMS. The reduced value is same as that of the value of original CN as in this case the complete original CN was rejected by the recipient.

Question 4: If any original Credit note was rejected by the recipient and supplier furnishes the same credit note in GSTR-1A of same tax period or in the amendment table of GSTR-1/IFF of any future tax-period, till the specified time limit, then what impact it will have on supplier’s liability?

Answer: At first instant the supplier’s liability will be added back in the open GSTR-3B return, because of original credit note rejection by the recipient. However, as the supplier furnishes the same credit note in GSTR-1A of same tax period or in amendment table of GSTR-1/IFF in any subsequent period, supplier’s liability for this amendment will get reduced again corresponding to the value of amended CN (which in this case is same as original). Thus, net effect on liability of supplier will be only once.

4. AAR:

(i) AAR On Time limit of availing ITC has been applicable to Bill of entries also

(Applicant – M/s. Adi Enterprises)

• The AAR held that a Bill of Entry qualifies as a “tax invoice” under Section 31 read with Rule 46, since it contains essential particulars such as description, quantity, value, and tax charged, and noted that the import of goods constitutes an inter‑State supply attracting IGST on the importer; it further observed that the provisions of Section 31 of the CGST Act apply mutatis mutandis to the IGST Act.
• Noted that while Section 16(2)(a) refers to “tax invoice or debit note or such other tax‑paying documents as may be prescribed” (which would include Bill of Entry under Rule 36(1)(d)) of the CGST Rules Section 16(4) expressly limits the time‑barred documents to “invoice or debit note” However, observing that Section 20 of the IGST Act makes the CGST provisions mutatis mutandis applicable to IGST, the AAR held that the time limit under Section 16(4) extends to import‑related ITC as well. Emphasizing the purpose of Section 16(4)—to ensure timely ITC claims, prevent indefinite carry‑forward of credits, and maintain fiscal discipline—the Authority ruled that all forms of ITC, including that on imports, must satisfy the same conditions. It concluded that the term “invoice” in Section 16(4) must be interpreted to include any document evidencing tax payment, such as a Bill of Entry.
• The AAR answered the question in the affirmative, holding that the time limit under Section 16(4) applies to ITC claimed via a Bill of Entry.

Disclaimer:

This publication contains information for general guidance only. It is not intended to address the circumstances of any particular individual or entity. Although the best of endeavor has been made to provide the provisions in a simpler and accurate form, there is no substitute to detailed research with regard to the specific situation of a particular individual or entity. We do not accept any responsibility for loss incurred by any person for acting or refraining to act as a result of any matter in this publication.

(Author is a well known Chartered Accountant practicing in Direct and Indirect Taxes at Ahmedabad)