2025 (11) TMI 1419 - HC - GST

Refund of wrongly paid IGST allowed; limitation under Section 54 and Rule 89(1A) held directory, not mandatory

M/s. Merck Life Science Private Limited Versus The Union of India, Central Board of Indirect Taxes And Customs New Delhi, Assistant Commissioner of Central Taxes North West Division-1 Bengaluru.

HC held that tax wrongly paid as IGST to Central authorities, when the transaction was later treated as intra-State and tax was paid again to State ... Refund of tax wrongly/erroneously paid to the Central Authorities under the bona fide belief that it was Inter-State supply - rejection of refund on the ground that the refund application having been filed on 30.03.2024 was barred by limitation in terms of the provisions contained in Section 54 of the CGST Act - provisions contained in Section 54 of the CGST Act and Rule 89(1A) of the CGST Rules, 2017 are mandatory or directory - HELD THAT:- A plain reading of Section 77(1) of the CGST Act will clearly indicate that the taxpayer who pays tax to the Central Authority by oversight, inadvertence and erroneously, would be entitled to refund of the amount of taxes so paid in such manner and subject to such conditions as may be prescribed - A similar provision exists in the IGST Act which relates to Inter-State supply and Section 19(1) of the IGST Act also contemplates that, if an Integrated Tax on a supply considered by the taxpayer to be an Inter-State supply is subsequently held to be an Inter-State supply, such taxpayer shall be granted refund of the amount of integrated tax so paid in such manner and subject to such conditions as may be prescribed - Rule 89(1A) of the CGST Rules, 2017 stipulate that the refund claim under Section 77 of the CGST Act and Section 19 of the IGST Act would have to be made within a period of 2 years from the date of payment by filing an application in the prescribed format. As can be seen from the aforesaid Statement of Objections, payment made by the petitioner towards IGST to the Central Authorities have not been disputed by the respondents, who on the other hand only merely contend that the refund claim of the petitioner is barred by limitation. In fact, respondent Nos. 2 and 3 also admit that the petitioner had made payment to the State GST Authorities subsequent to the payment made to the Central GST Authorities. It is therefore clear that respondent Nos. 2 and 3 have admitted that the petitioner had made such payment in favour of the Central GST Authorities towards IGST prior to making similar payment to the State GST Authorities. As held by the High Court of Madras in Lenovo (India) Pvt. Ltd v. Joint Commissioner of GST [2023 (11) TMI 774 - MADRAS HIGH COURT] and the High Court of Andhra Pradesh in the case of M/s. Nspira Management Services Private Limited v. Assistant/Deputy Commissioner of Central Tax [2025 (10) TMI 107 - ANDHRA PRADESH HIGH COURT], Section 54 of the CGST Act and Rule 89(1A) of the CGST Rules, 2017 have been held to be directory and not mandatory. It is also significant to note that having regard to Article 265 of the Constitution of India, the respondent – Central GST authorities were not entitled to collect IGST form the petitioner, who was not liable to pay the same and consequently, upon the petitioner paying the same amount to the State GST authorities subsequently, the respondent–Centre was not entitled to retain the IGST and consequently, by applying the principles of restitution and unjust enrichment, the respondent – Centre was obligated to refund IGST back to the petitioner. The impugned orders passed by respondent No. 3 holding that the refund claim is barred by limitation is contrary to facts and law and the same deserves to be set aside by holding that the refund application/claim of the petitioner is within time and is not barred by limitation. Grant of refund in favour of the petitioner as sought for in the refund application filed by the petitioner - HELD THAT:- In this regard, it is pertinent to note that respondent No. 3 has not considered the refund claim of the petitioner nor passed any orders on the merits of the refund claim of the petitioner. Thus, after having held that the petitioner is entitled to refund of the amount undisputedly paid by him towards IGST and having paid exactly the same/identical amount to the State GST Authorities, since respondent No. 3 has not passed any orders on merits, it is deemed just and appropriate to set aside the impugned orders by holding that the refund claim is not barred by limitation and remitting the matter back to respondent No. 3 for passing appropriate orders on the refund application in accordance with law within a stipulated time frame, bearing in mind the observations made in the body of this order. It is held that the refund application/claim of the petitioner is not barred by limitation - The matters are remitted back to respondent No. 3 for passing appropriate orders on the refund application filed by the petitioner, bearing in mind the observations made in the body of this order and in accordance with law - petition allowed by way of remand. ISSUES PRESENTED AND CONSIDERED 1. Whether refund applications under Section 19 of the IGST Act read with Section 77 of the CGST Act and Rule 89(1A) of the CGST Rules are barred by the two-year limitation prescribed in Section 54 of the CGST Act where tax was paid to Central Authorities (IGST) but subsequently also paid to State Authorities (CGST+SGST) because the supply was intra-State. 2. Whether Section 54 of the CGST Act and Rule 89(1A) are mandatory (ousting other remedies) or directory (permitting relief in appropriate cases), particularly where the tax was collected or paid without authority of law and Article 265 is invoked. 3. Whether the Central Authority can retain IGST undisputedly paid when the claimant has paid an identical tax amount to the State Authorities (application of unjust enrichment/restitution principles and Article 265). 4. Whether procedural irregularities by tax authorities (failure to issue deficiency memos under Rule 90(3), acceptance of applications/acknowledgements, denial on technical grounds) justify quashing orders rejecting refund claims as time-barred. 5. The proper remedy and direction where limitation objection was the sole ground for rejection and the authority did not decide refund on merits. ISSUE-WISE DETAILED ANALYSIS Issue 1 - Limitation under Section 54/Rule 89(1A): Legal framework Section 54 prescribes a two-year period to file refund applications 'before the expiry of two years from the relevant date'; Rule 89(1A) prescribes that refund under Section 77/Section 19 be filed within two years from the date of payment of tax under the correct head (with transitional provision from date of notification). Precedent treatment The Court considered recent High Court decisions holding Rule 89(1A)/Section 54 to be directory in appropriate circumstances (e.g., Madras and Andhra High Courts) and the Gujarat High Court decisions applying the Limitation Act where tax was collected without authority of law. The judgment reviewed and followed the reasoning in those decisions rather than treating them as distinguishable. Interpretation and reasoning Textual reading of Section 54 ('may make application before two years') supports a directory character: the provision enables an assessee to make application within two years but does not rigidly oust relief beyond two years in appropriate cases. Rule 89(1A) prescribes filing periods but the statutory scheme (and the Rule 90(2)/(3) mechanism for completeness/deficiency notices) reflects that procedural steps and acceptance of documents by the proper officer affect reckoning of time. The Court also relied on notifications excluding COVID-period from computation of limitation, and administrative circulars clarifying the relevant date and applicability. Ratio vs. Obiter Ratio: Where tax has been indisputably paid to the Central Authority and then the identical tax paid to the State Authority because the supply was in fact intra-State, the limitation under Section 54/Rule 89(1A) is not an absolute bar; refund applications filed beyond two years may be entertained in appropriate cases (Section 54/Rule 89(1A) are directory in such contexts). Obiter: Broader observations on the scope of Rule 89(1A) illustrations, and discussion of prospective vs retrospective operation of Supreme Court judgments, are persuasive but not essential to the core holding. Conclusions on Issue 1 The impugned orders rejecting refund claims as barred by limitation are unsustainable; the refund applications are not barred by Section 54/Rule 89(1A) in the factual matrix where IGST was paid though the supply was intra-State and identical tax was paid to State Authorities. The matter is remitted for fresh consideration. Issue 2 - Applicability of Article 265, payment without authority of law, and Limitation Act Legal framework Article 265 prohibits levy or collection of tax without authority of law. Where a charge is declared invalid (or tax collected without authority), restitution principles and Limitation Act provisions (e.g., Section 17 concerning relief from consequences of a mistake) are engaged. Precedent treatment The Court relied on High Court precedents (including Gujarat) holding that amounts collected without authority of law are not 'tax' for purposes of the special statute's limitation and that Limitation Act principles may govern refund claims made under mistake of law; these precedents were followed. Interpretation and reasoning If payment to Central Authorities was made though the taxpayer was not liable to pay IGST (supply was intra-State), that payment is in substance a payment under mistake of law and the Central Authority cannot retain the identical amount also received by State Authorities. Article 265 and restitution/unjust enrichment principles require refund unless some other statutory bar applies. Where Revenue admits excess payment but relies solely on limitation, the statutory limitation cannot be mechanically invoked to preclude restitution in such circumstances. Ratio vs. Obiter Ratio: Where tax is paid without authority of law (or under a mistake of law) and the identical tax has been paid to the correct authority, the collector (Central Authority) is not entitled to retain the amount; restitution principles require refund and limitation under the special law does not necessarily defeat the claim. Obiter: Detailed examples and cross-references to other authorities about interplay with appellate processes and taxation notifications are explanatory. Conclusions on Issue 2 Central Authorities were not entitled to retain the IGST amounts undisputedly paid where the petitioner subsequently discharged the correct tax to State Authorities; refund on the basis of restitution/unjust enrichment is warranted subject to merits to be considered afresh by the authority. Issue 3 - Procedural obligations, Rule 90(2)/(3) and administrative duty to assist Legal framework Rule 90(2)/(3) mandates scrutiny within 15 days and issuance of deficiency memo (Form RFD-03) if application is incomplete; CBDT/Central Board circulars and departmental circulars require officers to assist taxpayers, avoid dilatoriness in granting refunds and to facilitate rectification of defects. Precedent treatment The Court adopted the approach in Madras/Andhra decisions that procedural irregularities (failure to issue deficiency memo, issuance of show-cause without prior deficiency notice, inconsistent acceptance of documents) weigh against treating an application as belated. Interpretation and reasoning Where the officer accepted applications (acknowledgement) and in at least one instance processed the application after receiving documents at personal hearing, it was inconsistent and unfair for the authority to later contend that supporting documents were belated and that limitation began only when all documents were filed. Rule 90(3) required the officer to call for rectification; departmental circulars impose a duty to assist claimants. Failure to follow these procedures undermines reliance on limitation as a ground for rejection. Ratio vs. Obiter Ratio: Procedural non-compliance by the proper officer (failure to issue deficiency memo and inconsistent acceptance of documents) vitiates a limitation objection and requires remand for fresh adjudication in accordance with Rule 90 and administrative guidance. Conclusions on Issue 3 The impugned orders were procedurally flawed: the authority ought to have issued deficiency memos or acknowledged completeness consistently; it could not, after acceptance in part, adopt a contrary position to reject claims as time-barred. The matter is to be reconsidered after compliance with the prescribed procedure. Issue 4 - Remedy and directions Interpretation and reasoning Given that the Central Authority did not decide refund claims on merits and limited itself to finding claims time-barred, and in view of admitted undisputed payments and relevant precedents and circulars, the appropriate remedy is to set aside the impugned rejection orders and remit the refund applications to the Central Authority for fresh consideration in accordance with law, rules and administrative circulars within a defined time frame. Ratio vs. Obiter Ratio: Quashing limitation-based rejections and remitting for merit adjudication is the appropriate relief where payments are undisputed, procedural defects exist, and the statutory limitation is directory in the circumstances. Conclusions on Issue 4 The impugned orders rejecting refund claims as barred by limitation are set aside. The Central Authority must reconsider and decide the refund applications on merits in accordance with Section 19/Section 77, Rule 89(1A), Rule 90, the Board circulars and Article 265/ restitution principles within the time directed by the Court (remittal period specified for administrative compliance). Cross-references See Issue 1 and Issue 2 (interplay between limitation provisions and Article 265/restitution); see Issue 3 for procedural preconditions that affect limitation reckoning; remedy in Issue 4 follows from conclusions in Issues 1-3.