Prasad, an Additional Secretary in the ministry and who has been given an extension for two months till July, was at the centre of a row after a newspaper report claimed that he was "tutoring" the witnesses.
The newspaper also uploaded the conversation in public domain where he is purportedly conveying the questions as well as answers to one of the witnesses questioned by him in connection with an enquiry related to missing documents in Ishrat Jahan case.
He said no evidence has been produced establishing that the officer testified by him was being tutored during the alleged conversation.
"All officers enquired by me are or have been senior officers in the government and are fully capable of answering questions relating to the probe on their own and there is no question of the alleged tutoring.
"I have conducted a free and fair enquiry which my enquiry report will reveal," he said in a statement.