A bench of justices B D Ahmed and Sanjeev Sachdeva sought response from Centre within four weeks and posted the matter for further hearing on October 14.
The expert committee recomendations were submitted before the bench by petitioner NGO Centre for Public Interest Litigation (CPIL).
The affidavit filed by CPIL alleged that in a bid to reject the new alignment on the ground that it was only on paper, the report of ground survey carried out in 2009 was concealed.
The affidavit said the Commissioner of Railway Safety had also refused to give clearance for starting passenger services on the recently completed Lumding-Silchar line of Northeast Frontier Railway, declaring the line unsafe on account of instability.
It also alleged vested interest on the part of serving and retired senior Railway officers for preventing proper review of alignment for the Kashmir project over the past seven years from 2008 to 2015.
The Board had said that the committee's report does not provide what would be the proposed expenditure to be incurred for implementing the panel's recommendations.
It had said a "proper assessment for good construction status of alignment in this area shall require at least five years and would entail an expenditure of about Rs 300 crore".
The Board affidavit claimed that the existing alignment is "well researched, well investigated line where work is progressing successfully without mishaps or problems. The line is fully safe, survivable and stable".