General Secretary of hardline Hurriyat and chairman of Democratic Freedom Party (DFP) Shabir Ahmad Shah was taken into custody by police from his Sanat Nagar residence and was lodged at Rajbagh police station, they said.
The police action comes days after hardline Hurriyat asked people to offer funeral prayers in absentia today for the three militants who were killed in a 48-hour long gunbattle at Pampore early this week.
The Hurriyat had also called for a sit-in protest at every district headquarters after the Friday prayers and a general strike on February 27 to protest registration of sedition charges against the Kashmiri Scholar Prof S A R Geelani, alleged harassment of Kashmiri students in Delhi and the detention of JNU students.
However, the Hurriyat said some leaders managed to reach the Khankah at Pampore despite police crackdown and led the funeral prayers for the militants.
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Chairman of moderate Hurriyat Conference Mirwaiz Umar Farooq was also put under house arrest at his Nigeen residence in the outskirts of the city.
He said former Chairman of Hurriyat Prof Abdul Gani Bhat chaired the meeting and later tried to take out a march which was scuttled by police.
The Hurriyat leaders were carrying placards which read "revoke AFSPA and stop harassing Kashmiris".
Earlier, the spokesman said the hurriyat passed a resolution which condemned the arrest of Geelani and JNU students under sedition charges, "growing intolerance, frequent restrictions on the activities of separatist leaders.