JKLF chairman Mohammad Yasin Malik was arrested on 28 May from his residence in Srinagar in the summer capital of Jammu and Kashmir, the police said.
A police official said Malik has been shifted to central jail in Srinagar. He was arrested from his residence in Maisuma near Lal Chowk this morning.
The JKLF chairman had on Saturday visited the residences of slain Hizbul Mujahideen militants Sabzar Ahmed Bhat and Faizan Muzaffar in Tral area of south Kashmir's Pulwama district.
The two militants were killed in an encounter with the security forces in Soimoh area of Tral on Saturday.
Malik and chairmen of both factions of Hurriyat Conference, Syed Ali Shah Geelani and Mirwaiz Umar Farooq, have called for a two-day shutdown in the Valley to protest the killing of the two militants and the use of "brute force" against the protestors.
The separatist trio has also called for a march to Tral on Tuesday to pay tributes to the two militants.