"Whatever Supreme Court has observed, we will reply to it in our affidavit before May 6," he said.
Sinha said he would explain circumstances in which he went to the law minister's office.
Earlier on Tuesday, the agency drew flak from the Supreme Court for sharing its status report with the law minister and senior officials of the PMO and the coal ministry.
The apex court said that sharing of information with the government about the probe into the scam has "shaken the entire process" and CBI need not take instructions from "political masters" on their probe.
Following the comments of the apex court, Sinha went into a huddle with his senior officers to decide the future course of action.
Emerging from a 30-minute meeting at his North Block office, Sinha said he would respond to all queries raised by the Supreme Court on Tuesday in his affidavit as directed.
When asked whether he would demand more autonomy from Supreme Court, Sinha said, "It is a matter between government and judiciary, I cannot comment on that."
He said it is for them to take a call on what type of autonomy needs to be given to the investigating agency and under what circumstances it should interact with the political masters.