The agency charged them of allegedly receiving funds from Pakistan to carry out terrorist activities and stone pelting in 2010 and 2016.
The charge sheet, running into 200 pages, named Malik, as well as the founder and President of the Jammu and Kashmir Democratic Freedom Party Shabir Shah, Dukhtaran-e-Millat chief Asiya Andrabi, All Party Hurriyat Conference General Secretary Masarat Alam and former MLA Rashid Engineer.
Malik was produced before the court while others were to be produced later when the anti-terror agency submitted the charge sheet in the case before a special NIA court of judge Rakesh Kumar Syal.
Malik was arrested on April 4 this year for his role in fomenting unrest in Kashmir during separatist agitations in 2010, and in 2016 after the killing of Hizbul Mujahideen commander Burhan Wani.
Submitting the charge sheet, the agency said fresh material have surfaced in the form of social media evidence, call records, oral and documentary evidence.
"New material shows the relationship of the persons charge-sheeted with the cross border accused Hafiz Saeed (co-founder of Lashkar-e-Taiba and the chief of Jama'at-ud-Da'wah) and Syed Salahudeen (the head of Hizb-ul-Mujahideen)," said the NIA.
The court will take cognizance of the matter on October 23.
The NIA in 2017 arrested several separatists belonging to the two factions of Hurriyat Conference led by Mirwaiz Umar Farooq and Syed Ali Shah Geelani, respectively, for terror funding.
In its first charge sheet filed last year, the agency named Geelani's son-in-law Altaf Fantosh, Kashmiri businessman Zahoor Ahmed Shah Watali, Naeem Khan, Raja Mehrajudin Kalwal, Bashir Ahmed Bhat, alias Peer Saifullah, Aftab Hilali Shah, alias Shahid ul Islam, Farooq Ahmed Dar, alias Bitta Karate, Mohammad Akbar Khandey, alias Ayaz Akbar and Javed Ahmed Bhat, among others.
The NIA had registered the case in May 2017 against various separatist leaders who were acting in connivance with terrorist organisations like Hizb-ul-Mujahideen, Dukhtaran-e-Millat, and Lashkar-e-Taiba (LeT) for collecting funds through illegal means for funding terrorist activities and stone pelting in Jammu and Kashmir.
( With inputs from IANS )