The body was brought to the city airport in the afternoon from Bagdogra. Malik's wife accompanied the coffin.
It was later taken to his ancestral home at Madhyamgram in a hearse by road and subsequently to Nimtola crematorium at around 5 pm.
Malik was killed and four other policemen were seriously injured after allegedly Gorkha Janmukti Morcha (GJM) supporters, owing allegiance to its chief Bimal Gurung, fired at a police team at a forest area near Darjeeling yesterday.
West Bengal Higher Education Minister Partha Chatterjee and Food Minister Jyotipriyo Mallick received the body at the airport and offered floral tributes to the slain policeman.
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Both the ministers, along with other leaders and senior police officials, accompanied the coffin to his ancestral home where gun salute was given by the state police in the presence of the DGP Surojit Kar Purokayastha and other top officials.
As Malik's wife broke into tears, his family members, neighbours and a large number of people assembled at a club ground at Madhyamgram, where the coffin was kept for people to pay their last respect.
"Our son's soul will rest in peace only if Bengal remains undivided and Darjeeling continues to remain a part of it," Malik's parents said.
Gurung has been on the run since August after cases under the Unlawful Activities (Prevention) Act were slapped against him for his alleged involvement in several bomb blasts in Darjeeling and its adjoining areas.
This is the first incident of violence after the 104-day long indefinite shutdown in the hills was called off on September 26 by Gurung, following an appeal by Union home minister Rajnath Singh.