District judge Prasenjit Biswas gave the direction while rejecting the application of Chowdhury, who is Union Minister of state for Railways and the state Congress chief.
The Trinamool Congress had yesterday lodged an FIR against Chowdhury and 27 others for the murder of Badal Sheikh at Char Paraspur village under Jalangi police station on April 9.
Police sources had said that the killing occurred over a dispute on control of lease of a ferry ghat.