The NIA says noted Kashmiri businessman Zahoor Watali was the main conduit who acted as a go in between the embassy and the separatist leaders.
"A first secretary rank official used to meet many separatist leaders and also Zahoor Watali and we have evidence to show that money was paid to them," an officer dealing with the investigation told NDTV.
According to him they have enough oral, circumstantial evidences and the testimony of several witnesses against several Pakistani embassy officials. As the investigation in the case is still on, their names were not mentioned.
"We are trying to unravel a larger conspiracy," he added.
The NIA says this case is not about terror funding alone, it's about a conspiracy to wage war against India. "Terrorist organisations active in the Valley get support from Pakistan and Hurriyat is their political front," the chargesheet states.
The 12,794 page chargesheet also goes back to the beginning of terrorism in Kashmir in 1990s. "We have explained how protests are orchestrated, planned and executed in the Valley by these separatist leaders," disclosed an officer.
The chargesheet states stone pelting works like an organised sector - there are district, block, mohalla and tehsil level workers. "Mehraj ud Din Kanwal was a district president of Srinagar city. He used to organise protests. The money he used to receive from Pakistan he used to distribute among his workers or associates who used to organise pelting," the officer said.
According to him although most of the money received by conduits such as Kanwal was used to spread unrest in the Valley, part of it was also given to separatists leaders.
"We seized protest calendars during raids. We compared them and found out how they were planned on directions from across the border," said an officer.
The court is likely to take cognizance of the NIA charges against 12 accused, including seven Hurriyat leaders, on January 30.