In its FIR, the NIA mentioned that Hafiz Saeed and separatist leaders, including members of the Hurriyat Conference, have been acting in connivance with active militants of proscribed terrorist organisations Let, HM, Dukhtaran-e-Millat and other terrorist organisations for raising, receiving and collecting funds domestically and overseas through various illegal channels for funding terrorist activities in Jammu and Kashmir.
"The raids and searches were carried out in connection with the ongoing probe into the funding of militancy and separatist leaders and to unearth evidence to check linkages between LoC traders and hawala operators and their links with Hurriyat leaders", they said.
Mr Qayoom was questioned by the agency for over seven hours on Wednesday.
They said that the move was to counter the NIA's "harassment".
The NIa sleuths also raided the residence of Democratic Freedom Party (DFP) members Zameer Ahmad Sheikh and Razzaq Choudhary.
The agency had in July arrested seven separatist leaders and a prominent local businessman in connection with the probe into the terror funding by Pakistan-based terrorist groups to stoke unrest in the valley. Shakeel is patron of Islamic Student's League (ISL). Shabir Shah is at present in judicial custody after the Enforcement Directorate arrested him last month in connection with an earlier case of money laundering.
SHO Budgam Rafi Ahmad told Kashmir Reader, "The NIA team left the residence of Agha Hassan around 7pm and reached Srinagar safely". It said that the separatists and others whose houses and offices were raided today were "suspected of fuelling secessionist and subversive activities in Jammu and Kashmir".
However NIA did not arrest any of the suspects on Thursday.
Mittal said that during the NIA searches, "FDs (fixed deposits) worth over Rs 1 crore and a lot of incriminating material, suspect financial records, property-related documents and electronic devices were seized".
Jammu and Kashmir Liberation Front (JKLF) chairman and Separatist Kashmiri leader Yasin Malik was arrested in Srinagar on Thursday, a day after he, along with two other top separatist leaders Ali Shah Geelani and Mirwaiz Umar Farooq, threatened to stage a sit-in outside National Investigation Agency (NIA) headquarters in New Delhi. "A raid was also conducted at a premise at Gurugram". In south Kashmir's Bijbehara area, Ghulam Nabi Sumji's house was raided.