Malik was detained from his Maisuma residence in Srinagar. The arrest comes ahead of crucial hearing of Article 35-A in Supreme Court on Monday.
As per reports in local media, a JKLF spokesperson in a handout said that police raided residence of its chief and arrested him in the night. He was shifted to police station KothiBagh.
The group has condemned the incident.
The Supreme Court is scheduled to hear Article 35 A on Monday.
Article 35A of the Indian Constitution is an article that empowers the Jammu and Kashmir state's legislature to define “permanent residents” of the state and provide special rights and privileges to those permanent residents. It was added to the Constitution through a Presidential Order.
The arrest comes at a time when in a slew of crack down measures against Pakistan in the wake of Pulwama attack, the government has removed the security of all the separatist leaders.
The PDP on Friday criticised the government for its decision to withdraw security of protected persons in the state, terming it "non-sensical and vindictive in nature".
"The approach adopted by the authorities is vindictive in nature and that those at the helm are turning their eyes away from reality without any compunction. There is also chaos and confusion prevalent within the system," PDP general secretary Ghulam Nabi Lone Hanjura said.
He said on one side the government claims to have taken away the security of separatists like Syed Ali Geelani, Yasin Malik and Shabir Shah and on the other side these leaders claim to have never received any security cover.