Justice Harish Tandon directed the Special Investigation Team (SIT) headed by the West Bengal DGP to hand over all the material related to the inquiry to CBI.
The high court will monitor the progress of the CBI probe with Justice Tandon directing the agency to file reports before the court from time to time.
A prayer by state counsel Kalyan Bandopadhyay for stay on the order to allow the WB government to move an appeal was rejected by the court.
The court also observed that the SIT had not investigated the matter in the way it should have and said its role had not been satisfactory.
The court was critical of the role of the DGP for having given a clean chit to political leaders who were accused of making inflammatory speeches a few days before the murder of Sagar Ghosh, who fought and won as an Independent in the 2013 panchayat polls after being denied a ticket by the ruling TMC.