This was done to maintain law and order in the city, a police officer said.
Malik, chairman of the Jammu and Kashmir Liberation Front (JKLF), told IANS that police reached his uptown Abi Guzar office in the morning and seized him.
He said some other JKLF leaders were also arrested.
Separatist leaders, including hardliner Syed Ali Geelani and moderates like Mirwaiz Umer Farooq and Malik, have called for a boycott of the November-December election.
Earlier, Jammu and Kashmir police chief K. Rajendra Kumar told the media that security forces will not allow anyone to interfere with the peaceful conduct of assembly polls.