A bench of justices D K Jain and Madan B Lokur asked the Centre, Cairn India Ltd and other parties to file their couter affidavits within four weeks.
The court had issued a notice to Centre and the companies on April 27 but they failed to file their responses on a PIL seeking a CBI probe into the reasons for ONGC and government in "not asserting" their legal rights on the issue.
The bench said it would be difficut to reverse the deal but it would look into the allegation after a response is filed in the case.
"We will take note of what has happened," the bench said.
The bench was hearing a PIL filed by a Bangalore resident Arun Kumar Agarwal who alleged there was a clause in an agreement between Cairn group and ONGC that in case Cairn Group wanted to sell its shares in Cairn India, it would first offer the same to ONGC.
As per the clause, Cairn could sell its shares to other parties only after ONGC refused to buy the stake and ONGC, thus, had the right of first refusal (ROFR), he said.
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The petition alleged the decision on the deal had been made on "extraneous considerations" and without taking into account the relevant aspects.
The petition said had ONGC, which was Cairn India's joint venture partner, been offered its ROFR for Cairn India's shares and had it exercised its right, the exchequer would have benefitted by over Rs one lakh crore.