District judge Poonam A Bamba allowed the agency to interrogate in custody Altaf Ahmed Shah, popularly known as Altaf Fantoosh, along with six others to unearth the "complete conspiracy".
They may be taken to the valley for investigation for unearthing their modus operandi to raise funds to carry out secessionist and terror activities in the valley.
The agency, which sought custodial interrogation for 18 days, submitted that it had received information that Hafiz Saeed, head of Jamat-ul-Dawah, and separatists, including members of Hurriyat Conference, had been acting in connivance with banned outfits like Hizb-ul-Muzahideen, Lashkar-e-Taiba, Dukhtaran-e-Millat and others to raise and receive funds from inside and abroad through illegal channels, including hawala.
The money was being raised to fund separatist and terrorist activities in restive Jammu and Kashmir, it said.
"Accused are in criminal conspiracy against India by waging war against the State and they are involved in various offences punishable under Unlawful Activities (Prevention) Act," the agency said.
It said that custody of Shah and other accused -- Ayaz Akbar, Peer Saifullah, Shahid-ul-Islam, Mehrajuddin Kalwal, Nayeem Khan and Farooq Ahmed Dar -- was required as they had to be confronted with each other and with other incriminating evidences.
It added that the accused were involved in creating unrest by way of anti-India demonstrations and bandhs, which were done on their and others' instructions.
Advocate Rajat Kumar, appearing for the accused, opposed the NIA plea claiming that the accused were falsely implicated and they have been cooperating in the probe which has been going on for the past one month.
Syed Ali Shah Geelani's close aides Tehreek-e-Hurriyat spokesman Ayaz Akbar and Peer Saifullah were arrested by the NIA from the valley.
Shahid-ul-Islam is the spokesman of the moderate Hurriyat Conference led by Mirwaiz Umer Farooq.
Hafeez Saeed, the Pakistan-based chief of the JuD, the front of the banned Lashker-e-Taiba (LeT), has been named in the FIR as an accused, besides organisations such as the Hurriyat Conference, Hizbul Mujahideen (HM) and Dukhtaran-eMilat.
The houses of those arrested had been raided by NIA sleuths last month.
The raids were part of the NIA's efforts at clamping down on separatist groups allegedly receiving funds for subversive activities in the valley.
The NIA had claimed that it recovered account books, Rs 2 crore in cash and letterheads of banned terror groups, including of the LeT and the HM, during the raids.