The Supreme Court said on Friday that the Central Vigilance Commission (CVC) must complete the probe against CBI director Alok Verma within two weeks.
The court was hearing Verma's plea challenging the government's decision to divest him of his powers and send him on leave.
Retired SC judge AK Patnaik has been tasked with supervising the enquiry and making sure it is completed on time.
M Nageshwar Rao, who has been named interim director of the agency, can handle routine tasks to keep CBI functioning, and should not take any major policy decisions in the meantime, said Chief Justice Ranjan Gogoi.
Both Verma and his deputy Rakesh Asthana, the top two officials at CBI, have been placed on administrative leave after they accused each other of corruption.
Opposition leaders have accused the government of using the CBI as a tool to settle scores with its political opponents. The Congress, led by Rahul Gandhi, is marching to the CBI headquarters to protest against Verma's removal.
In his petition, Verma had said his ouster illustrated why India's premier investigative agency needed to be shielded from its political masters.