The National Investigation Agency (NIA) filed the 1,279- page charge sheet before a designated court here and sought permission to continue its probe.
The judicial custody of 10 people arrested in connection with the case ended today.
Under the anti-terror law -- the Unlawful Activities (Prevention) Act -- the prosecuting agency has to file a charge sheet within 6 months, failing which the accused is eligible for bail.
They said 60 locations were raided and 950 incriminating documents seized. There are 300 witnesses in the case.
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The NIA had arrested Altaf Ahmad Shah alias Altaf Fantoosh, son-in-law of Syed Ali Shah Geelani; spokesperson of Mirwaiz Umer Farooq-led moderate Hurriyat Conference Shahid- ul-Islam; spokesperson of the Geelani-led faction of Hurriyat Ayaz Akbar and separatists Nayeem Khan, Bashir Bhat alias Peer Saifullah and Raja Mehrajuddin Kalwal.
Noted businessman Zahoor Ahmed Watali was also arrested by the NIA in connection with the case, which was registered after the valley was rocked by violent protests following the killing of Hizbul Mujahideen poster boy Burhan Wani in a gunfight with security forces in 2016.
The NIA accused Saeed and Salahuddin of fomenting trouble and sending funds to the valley through non-banking channels, they said.
The FIR named Saeed as an accused, besides organisations such as the Hurriyat Conference (factions led by Geelani and Mirwaiz Farooq), Hizbul Mujahideen and Dukhtaran-e-Milat.
The NIA also recorded confessional statements on the flow of money, especially from Pakistan, from four people accused in a case related to the funding of "terror activities" in Kashmir.
The statements given before a judicial magistrate had tightened the case against the separatists who allegedly funded stone-pelters and spread unrest in Kashmir, the officials said.