Facts of the Case:

In this case, for the tax periods March 2023, April 2023 and May 2023, the petitioner failed to file GST returns within the prescribed time. Consequently, the assessing authority passed best judgment assessment orders under Section 62 of the GST Act for the said months. Subsequent to the assessment orders, the petitioner filed the returns along with payment of tax, and claimed to have paid interest and late fee as well. Despite this, the respondent authorities initiated recovery proceedings based on the assessment orders.

Aggrieved by such recovery, the petitioner approached the High Court contending that, in view of Section 62(2) of the GST Act, once the returns are filed within the prescribed time along with payment of dues, the assessment orders must be treated as deemed withdrawn. The petitioner specifically argued for May 2023, the returns were filed within 120 days, and therefore the assessment order dated 12.07.2023 stood automatically withdrawn, for March 2023, although returns were filed beyond 60 days, the time limit was subsequently extended to 120 days by amendment w.e.f. 01.10.2023, which should be treated as retrospective.

Issue:

Whether the best judgment assessment orders passed under Section 62 of the GST Act for March 2023, April 2023 and May 2023 could be treated as deemed withdrawn on account of subsequent filing of returns and payment of tax, interest and late fee, particularly in light of the amendment extending the time limit from 60 days to 120 days.

Held that: The Court held that the petitioner had substantially complied with the requirements of Section 62 of the GST Act by filing the pending returns and paying the tax dues. Insofar as the month of May 2023 is concerned, the returns were filed and taxes were paid within the extended period of 120 days and, therefore, by virtue of Section 62(2) of the GST Act, the assessment order dated 12.07.2023 stood deemed to have been withdrawn. With respect to the month of March 2023, although the returns were filed belatedly when the statutory period was 60 days, the subsequent amendment extending the time limit to 120 days was held to be beneficial in nature and was treated as having retrospective effect, thereby curing the defect and bringing the petitioner within the fold of compliance under Section 62(2).

As regards the month of April 2023, the Court noted that the returns were filed beyond the extended period of 120 days by a marginal delay of 12 days. Considering the facts and circumstances of the case, and following earlier judgments of this Court as well as the Madras High Court, the Court held that such marginal delay was liable to be condoned.

The Court emphasized that the petitioner had already discharged the tax liability and that procedural lapses should not defeat substantive compliance. Consequently, the Court declared that all the assessment orders passed under Section 62 for the months of March 2023, April 2023 and May 2023 were deemed to have been withdrawn, subject to verification of payment of interest and late fee.

The Court reinforces that once a registered person files the pending returns and pays the tax, interest and late fee within the prescribed period, the best judgment assessment under Section 62 stands deemed withdrawn by operation of law.

Case name: Meka Dredging Company Private Limited Versus The Deputy Assistant Commissioner-II, Amalapuram, The Assistant Commissioner State Tax, Amalapuram, The Deputy Commissioner State Tax, Andhra Pradesh, The Commissioner of State Tax, Commissionerate of Commercial Taxes, Government of Andhra Pradesh, The Union of India. dated 31.12.2025

To read the complete judgement 2025 Taxo.online 3558