The agency told Additional Sessions Judge Tarun Sherawat that Pakistan-based outfits have been passing on money through hawala channels and alleged that officials of country's High Commission were also playing an active role.
The National Investigation Agency (NIA) had on January 18 filed its 12,794-page charge sheet, along with annexures, against 12 people including Lashkar-e-Taiba chief Hafiz Saeed and Hizbul Mujahideen head Syed Salahuddin. Both Saeed and Salahuddin are absconding, it said.
"A conspiracy under the supervision of Pakistan-based organisations was hatched. The accused persons were working in connivance with Saeed and Salahuddin to raise funds for the terror activities," special public prosecutor and senior advocate Sidharth Luthra, appearing for NIA, said.
The submissions were made by the agency when the court asked what evidence they had gathered to try the accused.
The agency alleged that High Commission officials were passing money through arrested businessman Zahoor Watali, who would hand it over to separatists after deducting his cut. He is currently in judicial custody.
Besides Pakistan-based terrorists Saeed and Salahuddin, and Watali, the agency has also named hardliner Syed Ali Shah Geelani's son-in-law Altaf Shah alias Altaf Fantoosh, Bashir Ahmad Bhat and photo journalist Kamran Yusuf, who has been identified along with Javed Ahmad Bhat as a stone pelter.
Hurriyat Conference leaders Nayeem Ahmad Khan, Farooq Ahmad Dar alias Bitta Karate, Mohammad Akbar Khanday and Raja Mehrajuddin Kalwal have also been charged by the agency.
It alleged that the arrested accused were associated with "Hurriyat Conference and were prominent members of the society and that they had conspired to generate funds for the terror activities to oppose the lawful government of Jammu and Kashmir".
The NIA also submitted that a calendar, allegedly issued by the Hurriyat Conference, was recovered from Altaf Ahmad Funtoosh, mentioned the activities they conduct.
Letter heads of Hizbul Mujahideen were recovered from some of the arrested accused, the agency claimed, adding that Geelani had termed Afzal Guru a hero of Kashmir.
The court posted the matter for consideration of the charge sheet on February 1.
The NIA has alleged that Watali brought money from offshore accounts without any explanation. "There is an anti terror operation and suddenly the stone-pelting is organised. Mob is not spontaneous but have been funded by these organisations," the agency said.
The evidence also include the videos of the sting operation done by some news channels showing how the funds are raised, the NIA claimed.
The ten arrested accused, who are currently in judicial custody, were produced before the court.
The NIA said that a number of places were searched during the investigation which led to the recovery of various incriminating documents and other evidences which relate them to the terror organisations and the funding for the terror activities.
The charge sheet has charged all the 12 accused persons with criminal conspiracy, sedition, and under stringent provisions of the Unlawful Activities (Prevention) Act.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.