Petitioner Company had original filed return of income u/s 139(1) for AY 2015-16 and 2016-17. Subsequently, another company came to be merged with the petitioner company as per the scheme of amalgamation approved by the NCLT w.e.f 1.1.2015. The Company filed physical return of income, however the same was not accepted by the department as the time limit to file revised return had expired. The Court held that, the order of NCLT provided for filing of revised return and therefore, the company was eligible to file revised return. Further, it held that section 139(5) is not applicable to cases where revised returns are required to be filed pursuant to the approval of scheme of amalgamation by competent court. It also held that Rule 12(3) requiring filing of return of income electronically was not applicable to cases where the revised returns are require to be filed pursuant to the approval of scheme of amalgamation by competent court. Accordingly, the Court held that merely because the website of the Department was not accepting the return of income, cannot make the assessee remediless and that the Department to accept the revised returns. (AY. 2015-16, 2016-17)(WP No. 25314, 25315 of 2018 dt. 30.04.2019)