Maksur Analytical Systems Thr. Its Partner Makarand S. Gothe vs Union Of India Thr. Ministry Of Finance (Department Of Revenue ) And Ors

CNR No : HCBM010214042026

47-WP-7551-2026.doc
IN THE HIGH COURT OF JUDICATURE AT BOMBAY
CIVIL APPELLATE JURISDICTION
WRIT PETITION NO. 7551 OF 2026
Maksur Analytical Systems
through its Partner Mr. Makarand Shrikant Gothe
Regd. Office : Ground floor, 006, Building No.A-3,
PALA, Empire Industrial Hub, Plot No.22, MIDC,
Ambarnath Industrial Area, Chikoli,
Ambarnath (West), Dist.: Thane 421505
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Versus
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Union of India
through Ministry of Finance
(Department of Revenue)
No.137, North Block, New Delhi-110001
The Additional Commissioner (Appeals Thane)
Central Goods & Services Tax,
th th
8 & 12 Floor, Lotus Infocentre,
Near Parel Station, Parel (E), Mumbai-400012
The Assistant Commissioner
Central Goods & Services Tax,
Division IV, Thane Rural Commissionerate,
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3 Floor, Vardan Trade Centre,
MIDC Wagle Industrial Estate,
Thane (West)-400604
The Superintendent,
Central Goods & Services Tax, Range 3,
Division 4, Thane Rural Commissionerate,
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3 Floor, Vardan Trade Centre,
MIDC Wagle Industrial Estate,
Thane (West)-400604.
Manisha
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Digitally signed by
MANISHA
BALKRISHNA
TALEKAR
Date: 2026.11.03
18:09:05 +0530
MANISHA
BALKRISHNA
TALEKAR
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47-WP-7551-2026.doc
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Mr. Anant Bobe, for the Petitioner.
The Commissioner of Customs Mumbai-III,
(Imports),
INBOM4, Air Cargo Complex, Sahar,
Andheri (E), Mumbai 400099
Mr. M. P. Sharma a/w Ms. Mamta Omle, for the Respondent Nos.3
and 4.
Mr. Ram Ochani a/w Mr. Abhishek Mishra, for the Respondent No.5.
..…
CORAM : M. S. KARNIK &
SANDESH D.PATIL, JJ.
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DATE : 29 OCTOBER 2026
JUDGMENT [PER SANDESH D. PATIL, J.]
1. By the present Writ Petition, the Petitioner is seeking
directions to the Respondent Nos.1 to 5 to reconcile and give effect
to the Integrated Goods and Service Tax IGST amounting to
1,19,38,621/- paid by the Petitioner on import of the goods at the
point of entry during the financial year 2019-2020 by duly reflecting
the same in the Petitioner’s Electronic Credit Ledger on the GST
Portal.
2. The contention of the learned Counsel for the Petitioner is
that the IGST paid on the imports are required to be electronically
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47-WP-7551-2026.doc
transmitted from the ICAGATE system. It is submitted by learned
Counsel for the Petitioner that owing to systematic and technical
glitch in integration between ICEGATE and GSTN, the IGST paid on
imports by the Petitioner has not been correctly reflected in the GST
portal. This non-reflection is not attributable to any omission,
misstatement, or default on the part of the Petitioner, but is solely the
result of a failure of the electronic systems maintained by the
Respondents themselves. The Petitioner, in response to the
discrepancy notice for the Financial Year 2019-2020, furnished
complete details of IGST paid on imports along with supporting Bills
of Entry and reconciliation statements. Despite the availability of
such primary and unimpeachable evidence, the Respondents have
failed to either rectify the technical glitch or undertake reconciliation
of IGST paid vis-à-vis Input Tax Credit (ITC), whether manually or
electronically, and have instead proceeded based on incomplete and
inaccurate system-generated data.
3. It is contended by learned Counsel for the Petitioner that the
Respondents have proceeded to pass a series of mechanical, arbitrary,
and legally unsustainable orders and notices, solely based on
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incomplete system-generated data, without considering the
substantive evidence on record. The impugned actions have resulted
in grave prejudice to the Petitioner leading to a situation where the
Petitioner is effectively subjected to a double financial burden, i.e.,
payment of tax at the time of import and denial of corresponding
credit thereafter. The impugned demand, being founded entirely on a
technical glitch and system discrepancy, is arbitrary, unreasonable,
and liable to be set aside, with a direction for proper reconciliation
and reconsideration of the matter on merits after such reconciliation.
4. In this premise, the Petitioner has filed for quashing and
setting aside the Adjudication Order (OIO) No. 131/DSM/AC/DIV-
IV/2024-25, dated 29.08.2024, and quashing and setting aside of the
Order in Appeal No. DS/ADC/152/APPEALS THANE/TR/2025-26
dated 29.01.2026.
5. Learned Counsel for the Petitioner relied upon the Judgment
of the Calcutta High Court in the case of Amar Iron Udyog Pvt. Ltd.
1
Vs. Union of India .
1
2026 SCC OnLine Cal 6356
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6. Learned Counsel for the Respondent – Revenue Authorities
has strongly opposed the Petition. He contended that the impugned
Order is passed in accordance of law and requires no interference.
7. We have heard learned Counsel for the parties. The non-
reflection of the IGST prima facie is a result of failure of integration
between ICEGATE and GSTN, both of which are electronic systems
maintained and controlled by the Respondent authorities.
Admittedly, the Petitioner has no role to play in such transmissions.
The Petitioner therefore cannot be made to suffer for technical or
systematic lapses attributable to the Authorities themselves. The
impugned Orders are therefore on the face of it unsustainable as the
same are solely based on non-reflection of the IGST on the GST
Portal. The Petitioner has produced before us the documents
supporting payment of tax. In these circumstances, denial of ITC to
the Petitioner mainly on the ground of technical glitch and that too
on the part of the Petitioner was not proper. In these circumstances,
it would be necessary to quash and set aside the impugned Order
and remand the matter to the Authorities to decide the same afresh
by giving the Petitioner the right to put forth all the documents in
support of his case. Hence, the following Order:
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ORDER
(i) The Adjudication Order (OIO) No. 131/DSM/AC/DIV-
IV/2024-25, dated 29.08.2024 and the Order in Appeal No.
DS/ADC/152/APPEALS THANE/TR/2025-26 dated
29.01.2026 are quashed and set aside.
(ii) The Respondent Nos.1 to 5 are directed to reconcile and
give due consideration to the Integrated Goods and Services
Tax (IGST) amounting to Rs. 1,19,38,621/-, paid by the
Petitioner on import of goods at the point of entry during the
Financial Year 2019-2020, by duly reflecting the same in the
Petitioner's Electronic Credit Ledger on the GSTN portal.
8. We make it clear that we have not gone into the merits of
the matter and as such all contentions of all the parties are kept
open.
9. In view of above, Writ Petition No. 7551 of 2026 stands
disposed of.
(SANDESH D. PATIL, J.) (M. S. KARNIK, J.)
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