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Central Goods and Services Tax (Third Amendment) Rules, 2025

Notification/Circular No.: Notification No. 13/2025–Central Tax, dated September 17, 2025

Applicable Act/Rule: Central Goods and Services Tax Act, 2017

Applicable Section/Rule: Rules 31A, 39, 91, 110, 110A, 111, 113, 37, 37A, 38, 42, 43, and associated forms (GSTR-9, GSTR-9C, GST APL series) of the CGST Rules, 2017

Effective Date: September 22, 2025 (unless otherwise specified in the notification)

Central Board of Indirect Taxes and Customs (CBIC), under powers conferred by Section 164 of the CGST Act, 2017, has notified amendments to the CGST Rules, 2017. These amendments introduce changes in refund provisions, ITC reporting, annual return formats (GSTR-9, GSTR-9C), and appeal procedures before the GST Appellate Tribunal.

Details of Changes

  1. Short Title and Commencement
  • These rules may be called the Central Goods and Services Tax (Third Amendment) Rules, 2025.
  • Effective from September 22, 2025, unless otherwise provided.
  1. Amendment to Rule 31A (Valuation of lottery, betting, gambling, horse racing)
  • In sub-rule (2), the figure “128” is substituted with “140”.
  1. Amendment to Rule 39 (Distribution of credit by Input Service Distributor)
  • Effective April 1, 2025.
  • In sub-rule (1A), after the words “section 9 of the Act”, the following is inserted:

“or under sub-section (3) or sub-section (4) of section 5 of the Integrated Goods and Services Tax Act, 2017.”

  1. Amendment to Rule 91 (Grant of provisional refund)
  • Effective October 1, 2025.
  • Sub-rule (2) substituted as follows:

“(2) The proper officer shall, based on system-identified risk parameters, issue an order in Form GST RFD-04 within seven days from the date of acknowledgement of refund application under Rule 90(1) or (2).

Provided that where refund is not sanctioned for recorded reasons, the officer shall proceed under Rule 92.

Provided further that an order issued in Form GST RFD-04 shall not require revalidation by the proper officer.”

  1. Amendment to Rule 110 (Appeal procedures – filing and acknowledgment)
  • In sub-rule (1):
    • After words “final acknowledgment”, insertion of reference to “Part A of Form GST APL-02A”.
    • Deletion of provisos.
  • In sub-rule (2):
    • Deletion of provisos.
  • In sub-rule (4):
    • Words “in Form GST APL-02” replaced with “in Part B of Form GST APL-02A”.
  1. Insertion of New Rule 110A – Procedure for appeals before Single-Member Benches
  • Key provisions:
    1. President or Vice-President may assign appeals not involving substantial question of law to Single-Member Benches.
    2. If during hearing, Single-Member Bench finds question of law involved, it shall return the appeal to Division Bench with reasons.
    3. Past precedents within the State must be considered before assigning.
    4. Monetary threshold of ₹50 lakh (as per Section 109(8)) applies to aggregated tax, ITC, fine, fee, or penalty for determining jurisdiction.
  1. Amendment to Rule 111 (Appeal documents)
  • In sub-rule (1):
    • After “final acknowledgment” insertion of “Part A of Form GST APL-02A”.
    • Deletion of proviso.
  • In sub-rule (2):
    • Proviso omitted.
  • In sub-rule (4):
    • Substitution of words “in Form GST APL-02” with “in Part B of Form GST APL-02A”.
    • Replacement of “self-attested copy” with “self-certified copy”.
  1. Amendment to Rule 113 (Orders of Appellate Tribunal)
  • Sub-rule (2) substituted:

“(2) The Appellate Tribunal shall issue, or cause to be issued, a summary of the order in Form GST APL-04A, clearly indicating the final amount of demand confirmed.”

  1. Amendments to Form GSTR-9 (Annual Return)

(a) Table 6 – ITC Details

    • New rows inserted for:
      • ITC of previous financial year utilized in current FY (Rule 37 & 37A).
      • Net ITC (new formula introduced).

(b) Table 7 – Reversals

    • Expanded to cover reversals under Rule 37A, Rule 38, Rule 42, Rule 43.

(c) Table 8 – Other ITC Information

    • New sub-rows introduced for ITC on imports availed in subsequent FY.
    • Auto-population logic revised.

(d) Table 9 – Tax Paid

    • Recast to show:
      • Tax paid through Cash
      • Tax paid through ITC
      • Difference between payable and paid amounts

(e) Tables 10–14 – Transactions of Subsequent Year

    • Aligns with extended deadline (November 30) for reporting amendments, debit/credit notes, ITC availed in subsequent year.

(f) Instructions

    • Updated to clarify reporting for FY 2022-23, 2023-24, and 2024-25.
    • Special clarifications for ITC reversals, re-availments, and transitional reporting.
  1. Amendments to Form GSTR-9C (Reconciliation Statement)
  • Part II – Turnover reconciliation:
    • New row inserted for supplies under Section 9(5) (E-commerce operator liability).
  • Part III – Tax payable vs. tax paid:
    • Expanded to show Section 9(5) supplies.
    • Distinction between tax payable in cash vs. through ITC.
  • Part V – Auditor recommendations:
    • Modification: “Cash” replaced with “Cash or ITC”.
  • New row added for late fee payable under Section 47(2).
  1. New Forms Introduced / Substituted
  • Form GST APL-02A (Acknowledgment of Appeal):
    • Part A – Provisional acknowledgment (filing reference, ARN, fee, etc.).
    • Part B – Final acknowledgment or rejection (registration details, tribunal bench allocation).
  • Form GST APL-04A (Order Summary by Appellate Tribunal):
    • Captures: demand confirmed/reduced, appeal outcome, remand details.
  • Form GST APL-05 (Appeal to Tribunal):
    • Substituted with revised format.
    • Requires detailed information on appellant, grounds of appeal, disputed amounts (tax, interest, penalty, fee).

Link: https://taxinformation.cbic.gov.in/view-pdf/1010462/ENG/Notifications

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