Malik who had warned to launch a protest against the NIA in Delhi was nabbed from his Abi Guzar office in Srinagar.
Malik has been taken to the central jail in the valley.
Yesterday, separatists Syed Ali Shah Geelani, Mirwaiz Umar Farooq and Yasin Malik had said that they will protest outside the NIA headquarters on September 9 against, what they termed as, 'vilification of Kashmiri' people by the investigation agency.
Malik had alleged that the Centre was foisting one issue or the other every month on the people of Kashmir.
Earlier in the day, NIA also raided the house of Separatist leader Shabir Shah's Personal Assistant Zameer Thakur, in connection with the J-K terror-funding case.
The NIA has recently been conducting raids and arresting people associated with the separatist leaders in connection with matter. (ANI)