Observing that CBI was like a "caged parrot", the court said it should stand up to all "pulls and pressures" and not share its probe with anyone including the Law Minister.
In a significant order after a three-hour hearing, the bench headed by Justice R M Lodha asked the government to make an effort to come out with a law before July 10 to insulate CBI from external influence and intrusion.
"The heart of the report was changed on suggestions of government officials," the court said in an apparent reference to the raging controversy over the sharing of the draft status report with political executive and joint secretaries in the Coal ministry and the PMO.
The CBI action had triggered a major political controversy with Opposition, particularly BJP, demanding the sacking of Law Minister Ashwani Kumar and resignation of Prime Minister Manmohan Singh.