It will also file a review petition on Friday, which, while not challenging the cancellation of licences, will seek a reconsideration of the court's declaration that the first-come first-served policy was per se constitutionally invalid.
Confirming the development, DoT Secretary R Chandrasekhar said: "We filed a clarificatory petition in the Supreme Court on Thursday. The review petition will be filed on Friday.
It will not challenge the cancellation of licences but will raise some questions on policy formulation, some specifics regarding policy statements in the judgment, and the role of the executive in policy-making."
Chandrasekhar said no decision had yet been taken on seeking a presidential reference. In the review petition, DoT has said it would argue the court findings encroached upon the exclusive domain of the executive to make policy.
It has argued the findings could be taken to be applicable to all natural resources. Applying the said principles for all natural resources could lead to arbitrary and absurd consequences, it said.
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