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The High Court allowed the appeal, set aside the impugned judgment of the ITAT, and remitted the matter back to the ITAT. The Court held that the ITAT's reasoning for denying jurisdiction to the Guwahati authorities solely based on the registered office in Calcutta was not correct. The location of the registered office, without other relevant material, is not conclusive in determining the principal place of business. The Court noted that if the assessee conducted all its business activities under the jurisdiction of the Guwahati authorities and not in Calcutta, then Guwahati could be the principal place of business. The Court also observed that while an objection regarding lack of jurisdiction should ideally lead to a reference to higher authorities under Section 124(2) of the Act, the AO had considered the objection and proceeded with the assessment. Given the stage, the Court found it inappropriate to refer the matter back to the AO for a Section 124(2) reference. Instead, it directed the ITAT to re-examine the issue of jurisdiction based on the materials on record and record its findings.
The Tribunal held that the provisions of Section 142 and sub-sections (2) and (3) of Section 143 have mandatory application in cases where the Assessing Officer, in repudiation of a return filed in response to a notice under Section 158BC(a), proceeds to make an inquiry. The Tribunal found that defects arising in such a scenario cannot be cured at a later stage due to the limitation provided in Section 143(2). The Court noted that the question of mandatory application of notice under Section 143(3) was decided in favor of the appellant in a previous appeal (ITA No. 40/2004). Consequently, the Tribunal held that Question 1 is answered in favor of the appellant and against the revenue. In view of this decision on Question 1, the Tribunal held that Question 2 does not arise. The appeal was allowed, and the impugned orders were set aside.
On Question No. 1 (Limitation), the Tribunal held that the High Court's order in Civil Rule No. 653 of 1996 did not constitute a stay of proceedings. The order merely directed that proceedings should continue but the final order should not be passed until the application under Section 127 was disposed of by the Commissioner. Therefore, the period of limitation could not be extended due to this order. The Tribunal also noted that the Commissioner disposed of the Section 127 application belatedly on October 15, 1996, and the period of limitation cannot be extended for apparent defaults on the part of the Commissioner. The Court has no power to extend the limitation period in exercise of writ jurisdiction, nor can Section 5 of the Limitation Act be applied. Thus, Question No. 1 was answered against the Revenue and in favour of the assessee, holding the assessment order barred by limitation. On Question No. 2 (Approval of Range DCIT), the Tribunal found the factual matrix inadequate to conclude that the approval was preceded by any deep-seated influence in the decision-making process. However, the Tribunal declined to answer this question as it lost its significance in view of the decision on Question No. 1.