Malik was arrested from Batmaloo bus stand when he was en route to Hyderpora residence of Geelani to meet him, a JKLF spokesman said.
He said Malik was initially taken to Kothibagh police station and later shifted to Central Jail Srinagar.
Condemning the arrest, JKLF spokesman said Malik was arrested more than six times by police since May 25.
Malik has been making efforts to bring various separatist organisations on one platform. He had met Geelani about a month back, after which leaders of two factions of Hurriyat Conference -- hardline faction led by Geelani and moderate faction led by Mirwaiz Umar Farooq -- along with Malik held a trilateral meeting.