Malik was killed on October 13 at Tukvar forest and four other policemen were injured during the raid when the clash with Gurung's supporters had taken place.
Days after it Darjeeling police had lodged a suo motu FIR against the GJM leader and others in connection with the killing.
"We have taken up the case. We will start our investigations into the death of SI Amitava Malik," state CID ADGP Rajesh Kumar told PTI.
"Gurung and his associates have been booked for their alleged involvement in violence, arson and killing of an on duty sub-inspector," a senior police officer said.
West Bengal Director General of Police Surajit Kar Purkayastha had visited Darjeeling after the incident to monitor the situation.
Gurung has been in hiding since August after cases under the Unlawful Activities (Prevention) Act were registered against him for his alleged involvement in several bomb blasts in Darjeeling and adjoining areas.