JKLF chief Yasin Malik was on Thursday arrested while Hurriyat leader Mirwaiz Umar Farooq was put under house arrest, a day ahead of the planned sit-in by the separatists outside the NIA headquarters in Delhi.
Malik was taken into custody from Srinagar and shifted to Central Jail till 11 September, officials said.
They said Mirwaiz was placed under house arrest to prevent the separatist leaders from going to Delhi on Friday.
Hurriyat hawk Syed Ali Shah Geelani has been under house arrest for the past several years now.
Malik, Geelani and Mirwaiz on Wednesday announced that they will hold a dharna outside the NIA office in Delhi and court arrest against the alleged harassment by the NIA.
The NIA has recently been conducting raids and arresting people associated with the separatist leaders in connection with alleged money laundering and some other cases.