The charge sheet was filed before a designated court in Delhi, with NIA seeking permission to continue its probe.
The main accused in the chargesheet, filed before the court of Additional Session Judge Tarun Sherawat includes Hafeez Saeed, the Lahore, Pakistan-based, head of "proscribed terrorist organisation Lashkar-e-Toiba and Amir of Jamaat-ud-Dawah".
The charege-sheet says that the NIA teams conducted searches at over 60 locations in Jammu and Kashmir, Haryana and New Delhi and seized over 950 documents and over 600 electronic devices.
Some 300 witnesses have been examined during the course of investigation.
All the accused have been charged with waging war against India, sedition, criminal conspiracy, and have been booked under various sections of Unlawful Activities (Prevention) Act or UAPA.
Others accused are Altaf Ahmad Shah, son-in-law of hardline Hurriyat Chairman Syed Ali Shah Geelani, Aftab Ahmad Shah, a close aide of moderate Hurriyat chief Mirwaiz Umar Farooq, and well-known businessman Zahoor Ahmad Watali.
At a press conference shortly after the NIA filed the chargesheet, Malik said arresting separatists was the government's tactic to have them hold a dialogue with the administration. "Analysis of documents and digital devices showed that the accused carried out terrorist attacks and orchestrated violence and stone-pelting as part of a well-planned criminal conspiracy", he said.
According to the NIA, the Hurriyat leaders and two stone pelters prepared "strategies and action plans" under the "overall guidance and instructions" from Saeed and Salahuddin for launching "violent protests" in Kashmir.
The agency has named Saeed, the Lashkar-e-Taiba founder and alleged mastermind of the 2008 Mumbai terror attack, and Salahuddin, the Hizbul Mujahideen chief, as the accused in its almost 13,000-page chargesheet.
"The money is routed through fake and bogus companies floated overseas and remitted to the Hurriyat leaders in Jammu and Kashmir".
The NIA recorded confessional statements on the flow of money, especially from Pakistan, from four accused.
Former Jammu and Kashmir Liberation Front militant Bitta Karate, photo journalist Kamran Yusuf and Javed Ahmed Bhat have also been named in the charge sheet.
While three of them have been formally arrested, the fourth one was detained and subsequently let off after he said he would turn approver, the officials said, declining to divulge their names.
Mr Farquhar used to be a lay preacher at Stowe Parish Church where Field is listed as a deputy warden. The causes of death for the couple, from Maids Moreton, have not yet been determined, officers said.
As Secretary, a post which he held for nearly a decade, Calcutta took a token salary of just Re one per month from the SGPC. Calcutta started his political life as an activist of the All India Sikh Students Federation in the early 1950s.
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