Earlier in the day, the NIA conducted fresh searches at nine locations in Jammu and Kashmir as part of its probe.
The residents of Shariatabad Budgam on thursday stormed into the residence of Aga Syed Hasan, senior Hurriyat leader where NIA slueths were conducting a raid and raised massive slogans against the investigating agency.
Among those whose premises were searched include separatist leaders Ghulam Nabi Sumji and Syed Aga Hassan Budgami, both close to hardline separatist leader Syed Ali Geelani.
Jammu and Kashmir Liberation Front chief Yasin Malik was arrested at Lal chowk, while Hurriyat (M) Chairman Mirwaiz Umar Farooq was put under house arrest. Sources said two houses and a shopping complex were raided by the NIA in Srinagar and Kupwara. The NIA is reported to have seized Rs. 2.2 crore in cash during the raids and also detected "suspicious" foreign transactions of about 100 crore during the investigation. The separatist leader, however, said his arrest would not break the spirit of the freedom loving people of the state.
The case was registered on issues of raising, receiving and collecting funds through various illegal means, including hawala channels, for funding such activities.
Malik was detained at his office a day after he threatened to march to the National Investigation Agency in New Delhi after separatists were arrested for their role in stone pelting in the Valley.
Day after Jammu and Kashmir Liberation Front chairman Yasin Malik addressed a joint press conference outside Jamia Masjid in Downtown Srinagar and dared New Delhi to keep the doors of Tihar jail open.
Zameer Ahman, a close aide of separatist leader Shabir Ahmad Shah who was arrested by the Enforcement Directorate on July 25, was quizzed at Gulshan Nagar-Nowgam in Srinagar.
After the NIA summoned Kashmir High Court Bar Association (HCBA) president Mian Abdul Qayoom to Delhi, the association on Thursday wrote an open letter to the Chief Justice of India. Kamran Yousuf, the journalist was arrested along with Javed Bhat from Kulgam by the NIA.