Voluntary tax payment and paid penalties under protest must be addressed through a manual rectification application rather than a writ remedy.

By | May 21, 2026

Voluntary tax payment and paid penalties under protest must be addressed through a manual rectification application rather than a writ remedy.

Issue

Whether a taxpayer can directly seek a writ remedy to quash an Order-in-Original and consequential recovery notices (Form GST DRC-13) when they claim the underlying tax liability was paid voluntarily and penalties were deposited under protest, or if they must first approach the proper officer for rectification under Section 161.

Facts

  • The petitioner filed a writ petition challenging an adverse Order-in-Original and the subsequent bank attachment/recovery actions initiated via Form GST DRC-13.

  • The petitioner asserted that the entire tax liability arising out of the relevant invoice had already been fully and voluntarily discharged.

  • In addition to the tax, the petitioner had also paid the disputed penalty amount under protest and was actively seeking a refund.

  • Respondent No.1 passed the primary Order-in-Original, and Respondent No.2 subsequently initiated the recovery mechanisms under Form GST DRC-13 to realize the dues.

  • The petitioner opted to approach the High Court directly via a writ petition to stay the recovery and set aside the assessment order.

Decision

  • Alternative Remedy Mandated: Held, yes. The High Court determined that the petitioner ought to first approach the proper officer to seek a rectification of the Order-in-Original and the consequential DRC-13 recovery notice.

  • Submission of Proof Required: Held, yes. The petitioner must submit all relevant supporting documents and evidence of voluntary tax and penalty payments before the rectifying authority.

  • Manual Applications Allowed: Held, yes. Recognizing technical limitations, the court directed that since the online portal might not permit an online rectification application, the proper officer must accept and entertain a manual application.

  • Writ Relief Declined with Liberty: Held, yes. The court declined to grant direct writ relief against the ongoing recovery and disposed of the petition, while reserving liberty for the petitioner to legally challenge the outcome of the rectification proceedings if they remain aggrieved.

Key Takeaways

Exhaustion of Statutory Remedies: High Courts will generally not entertain writ petitions against assessment and recovery orders if statutory rectification pathways (such as Section 161 of the CGST Act) are available to correct factual errors regarding prior tax payments.

Portal Limitations Cannot Block Justice: Structural or technical limitations on the online GST portal cannot strip a taxpayer of their statutory rights. If the portal does not support a necessary filing, the tax authorities are legally obligated to accept, process, and decide upon manual applications.

HIGH COURT OF TELANGANA
Biotech Pest Control India (P.) Ltd.
v.
Superintendent of Central Tax*
APARESH KUMAR SINGH, CJ.
and G.M.MOHIUDDIN, J.
WRIT PETITION No. 11164 of 2026
APRIL  15, 2026
Makaradh Prasad and C. Anvesh Kiran, Learned counsels for the Petitioner. Dominic Fernandes, Learned Senior Standing Counsel for the Respondent.
ORDER
1. Sri Makaradh Prasad, learned counsel appears for Sri C. Anvesh Kiran, learned counsel for petitioner.
Sri Dominic Fernandes, learned Senior Standing Counsel for Central Board of Indirect Taxes and Customs (CBIC) appears for respondent Nos.1 to 3.
2. The instant Writ Petition is directed against Order-In-Original dated 19.07.2024 passed by respondent No.1 and consequential recovery proceedings initiated by respondent No.2 under Section 79 of the Central Goods and Services Tax Act, 2017 (for short ‘the Act’) vide notice in Form GST DRC – 13 dated 09.03.2026.
3. According to the petitioner, it has fully discharged the tax liability arising out of Invoice No.150 dated 31.03.2019 and made voluntary payments totalling to Rs.1,87,544/- in Form GST DRC – 03 under Section 73(5) of the Act. Therefore, the petitioner has prayed for refund of the amount of Rs.40,000/- paid as penalty under protest. Certain documents in support thereof are annexed from pages 47 to 57.
4. In the aforesaid circumstances, upon hearing the learned counsel for the parties, we are of the view that the petitioner should approach the proper officer seeking rectification in the impugned Order-In-Original dated 19.07.2024 and the notice in Form GST DRC – 13 dated 09.03.2026 with all supporting documents. In case the portal does not allow filing of rectification application under Section 161 of the Act online, respondent No.1 shall entertain such application manually within a period of two (2) weeks and take a decision thereon within two (2) weeks thereafter. Needless to say, if the petitioner is aggrieved by the order, it will be at liberty to assail it in an appropriate proceeding in accordance with law.
Accordingly, the instant Writ Petition is disposed of. There shall be no order as to costs.
Miscellaneous applications, if any pending, shall stand closed.
Category: GST

About CA Satbir Singh

Chartered Accountant having 12+ years of Experience in Taxation , Finance and GST related matters and can be reached at Email : Taxheal@gmail.com