ITC Reversal Quashed as Section 16(5) Window Overrides Section 16(4) Limitation Period

By | November 5, 2026
ITC Reversal Quashed as Section 16(5) Window Overrides Section 16(4) Limitation Period
Issue Whether Input Tax Credit (ITC) reversed as time-barred under Section 16(4) of the CGST/TNGST Act remains allowable if the claim falls within the relaxation window prescribed under Section 16(5).
Facts
  • Assessee’s Profile: The petitioner is a registered dealer under the Goods and Services Tax (GST) framework.
  • ITC Reversal & Demand: The tax authorities initiated proceedings and issued an order reversing the petitioner’s ITC along with consequential demands, solely treating the claim as time-barred under Section 16(4).
  • Legal Challenge: The petitioner filed a writ petition challenging the ITC reversal order, contending that the ITC claim fell within the extended period/window permitted under Section 16(5).
Decision
  • The impugned order reversing the ITC was quashed to the extent it rested on Section 16(4) limitation, as the claim fell within the prescribed period under Section 16(5) [Paras 4 and 5].
  • The limitation under Section 16(4) cannot defeat ITC claims that are validly covered within the Section 16(5) window [Paras 4 and 5].
  • The Department was restrained from initiating any further proceedings based on limitation pursuant to the quashed order [Paras 4 and 5].
  • Consequential relief, including defreezing of bank accounts and granting refund or future tax adjustments, was directed [Paras 4 and 5].
  • Liberty was reserved for the Department to independently proceed against any discrepancies, wrong, excess, or fake ITC in accordance with law [Paras 4 and 5].
  • Decided in favour of assessee.
Key Takeaways
  • Overriding Effect of Section 16(5): Statutory relief provided under Section 16(5) overrides the general limitation period prescribed under Section 16(4) for claiming Input Tax Credit.
  • Protection of Timely Claims: Where an ITC claim falls within the Section 16(5) relaxation window, tax authorities cannot disallow or reverse the credit by invoking Section 16(4).
  • Scope for Merit-Based Verification: While disallowances based strictly on Section 16(4) limitation are invalid for claims covered under Section 16(5), the Revenue retains the right to verify the genuineness and correctness of the underlying ITC on merits.
HIGH COURT OF MADRAS
J Santhanam Contractor
v.
Assistant Commissioner (ST)
Krishnan Ramasamy, J.
WP No. 39002 of 2026
WMP Nos. 43786 and 43788 of 2026†
OCTOBER  6, 2026
Kabil Devi S. for the Petitioner. Ms. G. Dhana Madhri, Spl. GP for the Respondent.
ORDER
1. This Writ petition has been filed by the petitioner/taxpayer, who is registered dealer on the files of the respondent-Department under the provisions of the Goods and Service Tax Act, 2017 (GST Act)/ Central Goods and Services Tax Act ( CGST Act) as the case may be, challenging the orders passed by the respondent-Department, whereby, their claim of ITC was reversed/negatived and consequently, the petitioners have been directed to pay tax/penalty/interest.
2. When this Writ Petition is taken up for hearing, the respective learned counsel for the petitioner and learned Special Government Pleader for the respondent, would submit that the issue involved in the present Writ Petitions, has been squarely covered by the common order of this Court, dated 17.10.2024 passed in Sri Ganapathi Pandi Industries v. Assistant Commissioner (State Tax) (FAC) [2025] 171   (Madras)/W.P.Nos.25081 of 2023, etc., batch, wherein, this Court has categorically held in paragraphs 9 to 12 as under:
“9. The petitioners in all these Writ Petitions are registered dealers on the files of the respondent-Department under the provisions of the Goods and Service Tax Act, 2017/CGST Act 2017. Though the petitioners have filed GSTR-1 returns in time, however, insofar as claim of ITC is concerned, since the petitioners were faced with certain difficulties, such as Financial constraints (as there was complete lock down due to outbreak Covid-19) health related ailments, fire accidents, they were unable to file GSTR-3B returns, which prompted them not raising their claim ITC in time before the prescribed date. Whereas, the respondent- Department without considering such vital aspects and that reasons for the delay is not deliberate, issued the show cause notices to the petitioners, proposing to reverse the ITC availed and went to the extreme level of confirming the proposals contained in the show cause notices by passing the impugned orders, whereby, the claim made by the petitioners for ITC was reversed and the petitioners have been directed to tax/penalty/interest. Aggrieved against the impugned orders, the petitioners are before this Court by way of present Writ Petitions seeking for setting aside the impugned orders.

10. After the filing of these Writ Petitions, certain development took place, i.e. that 53 GST Council Meeting was held on 22.06.2024, and during the said Meeting, the GST Council recommended for extension of the deadline for availing ITC on any invoice or debit note under Section 16(4) of the CGST Act and this extension would be applicable to any GSTR-3B returns filed for the Fys 2017-18, 2018-19, 2019-20 and 2020-21 with a new deadline deemed to be as “30.11.2021”, to which, the Presidential Assent was also obtained by the Government of India on 16.08.2024, whereby, the financial proposals of the Central Government for the Financial Year 2024-25 was given effect to vide Finance Act, (No.2) of 2024, and in view of the aforesaid enactment, the Ministry of Finance (Department of Revenue) Central Board of Indirect Taxes and Customs, issued a Notification, bearing No.17 of 2024-Central Tax, dated 27.09.2024, pursuant to which, a Circular No.237/31/2024-GST was issued by the Central Board of Indirect Taxes and Customs, which was addressed to all the Principal Chief Commissioners /Chief Commissioners/Principal Commissioners/Commissioners of Central Tax (All), thereby, clarifying the issues regarding implementation of provision of sub-section (5) and sub- section (6) in Section 16 of CGST Act, 2017, the impugned orders are no longer sustainable and liable to be quashed. In this context, it would be apposite to refer to both Section 16(4) of the CGST Act, 2017, as well as amendment made to Section 16 (4) by interpolations of sub-sections 16 (5) and (6), and by insertion of sub-section (5) to Section 16, which are extracted herein under:-

Section 16 (4)

“A registered person shall not be entitled to take input tax credit in respect of any invoice or debit note for supply of goods or services or both after the thirtieth day of November following the end of financial year to which such invoice or debit note pertains or furnishing of the relevant annual return, whichever is earlier.”

Section 16 (5) :-

“Notwithstanding anything contained in sub-section (4), in respect of an invoice or debit note for supply of goods or services or both pertaining to the Financial Years 2017-18, 2018-19, 2019- 20 and 2020-21, the registered persons shall be entitled to take input tax credit in any return under section 39 which is filed upto the thirtieth day of November, 2021.”
10.1 Thus, a perusal of above Section 16 (5) makes it clear that ‘notwithstanding anything contained in sub-section 4, referred to above, in respect of any invoice or debit note for supply of goods or services or both pertaining to the Fys 2017-18 to 2020-21, the registered persons shall be entitled to take ITC in any return under section 39 which is filed upto th the 30 day of November, 2021.
10.2 Thus, this Court considering the fact that the issue involved in all these Writ Petitions is only with regard to the availment of ITC, which is barred by limitation in terms of Section 16 (4) of the CGST Act, and in the light of the subsequent developments took place, whereby, Section 16 of the CGST Act was amended and sub-section (5) was inserted to Section 16, which came into force with retrospective effect from 01.07.2017, the petitioners are entitled to avail ITC in respect of GSTR-3B filed in respect of FYs 2017-18, 2018-19, 2019-20 and 2020-21 as the case may be, on or before 30.11.2021, is inclined to quash the impugned orders.
11. Accordingly, this Court passes the following orders.
(i) The orders impugned in all Writ Petitions are quashed insofar as it relates to the claim made by the petitioners for ITC which is barred by limitation in terms of Section 16 (4) of the CGST Act, 2017 but, within the period prescribed in terms of Section 16 (5) of the said Act.
(ii) Therefore, the respondent-Department is restrained from initiating any proceedings against the petitioners by virtue of the impugned orders based on the issue of limitation.
(iii) In view of the fact that the impugned orders are quashed, the respondent-Department is directed to take immediate steps towards de-freezure of the concerned petitioners bank accounts, which have been freezed in furtherance of the impugned orders, by sending intimation to the concerned bankers.
(iv) In the event, in the interregnum, i.e. during the pendency of these Writ Petitions, if any orders are proposed to be passed towards recovery, same shall be dropped immediately upon production of the order copy by the petitioners, in whichever case, where, there is no interim order.
(v) It is also made clear that if at all, if there is any tax amounts were collected from the petitioners based on the impugned assessment orders from the cash ledgers/credit ledgers of the petitioners concerned, the same shall be refunded to them or by means of orders of this Court or even in the absence of any order from this Court, if any amount is deposited either in the cash ledgers/credit ledgers of the petitioners concerned, the same is permitted to be utilized/adjusted by the petitioners towards payment of future tax.
(vi) Insofar as the apprehension expressed by the learned Additional Advocate General for the respondent-Department that in certain Writ Petition apart from the issue on limitation, challenges have also been made to the order related to issues such as discrepancies in availing the ITC/wrong availment of ITC/excess claim of ITC/Fake ITC claim, as the case may be, or such other issues, liberty is be granted to the respondent-Department to proceed against the assessees/petitioners in furtherance of the impugned orders in accordance with law.
12. In the result, all the Writ Petitions are allowed on the aforesaid terms. No costs. Consequently, connected Miscellaneous Petitions are closed.
3. Therefore, the learned counsel for the petitioner would submit that the above said order will hold good for the present Writ Petition also and hence, prayed to dispose of the Writ Petition. The learned Special Government Pleader appearing for the respondent would fairly accede to the same.
4. In view of the above, this Court passes the following:
(i) The impugned order dated 21.02.2023 is quashed insofar as it relates to the claim made by the petitioner for ITC which is barred by limitation in terms of Section 16 (4) of the CGST Act, 2017 but, within the period prescribed in terms of Section 16 (5) of the said Act.
(ii) Therefore, the respondent-Department is restrained from initiating any proceedings against the petitioners by virtue of the impugned order based on the issue of limitation.
(iii) In view of the fact that the impugned order is quashed, the respondent-Department is directed to issue direction to the concerned bank to de-freezure of the petitioner bank account, if any, which have been freezed in furtherance of the impugned order, by sending intimation to the concerned bankers.
(iv) In the event, in the interregnum, i.e. during the pendency of this Writ Petition, if any orders are proposed to be passed towards recovery, same shall be dropped immediately upon production of the order copy by the petitioners, in whichever case, where, there is no interim order.
(v) It is also made clear that if at all, if there is any tax amounts were collected from the petitioner based on the impugned assessment order from the cash ledgers/credit ledgers of the petitioner concerned, the same shall be refunded to them or by means of orders of this Court or even in the absence of any order from this Court, if any amount is deposited either in the cash ledgers/credit ledgers of the petitioner concerned, the same is permitted to be utilized/adjusted by the petitioners towards payment of future tax.
(vi) If there is any challenge related to issues such as discrepancies in availing the ITC/wrong availment of ITC/excess claim of ITC/Fake ITC claim, as the case may be, or such other issues, liberty is be granted to the respondent- Department to proceed against the assessee/petitioner in furtherance of the impugned order in accordance with law.
5. Accordingly, the present Writ Petition is allowed on the aforesaid terms. No costs. Consequently, connected Miscellaneous Petitions are closed.