Malik and over 200 supporters marched to the city centre Lal Chowk against an alleged gun battle at Pathribal and other killings by security forces which the JKLF said needed to be probed independently.
Malik and his supporters reached Lal Chowk shouting slogans and carrying banners against "fake encounters" in Kashmir. Police used batons to intercept the protesters. Malik and 13 supporters were detained and sent to a police station.
Shops and other businesses were already closed in the area because of a shutdown called by hardline separatist leader Syed Ali Geelani.
Geelani accused the security forces of killing seven civilians in Kupwara district Feb 24. The army and police say all the seven were Pakistani terrorists. The state government has also said that the dead men were not locals.