The agency made the allegations in a charge sheet filed before District Judge Poonam A Bamba, who posted it for consideration on May 4.
The final report has alleged that Yusuf had hatched a conspiracy to received funds from Pakistan through hawala channels to spread terrorism in Jammu and Kashmir. The NIA has accused him of committing various offences punishable under Unlawful Activities (Prevention) Act.
Yousuf, 42, was posted as agricultural assistant in Budgam town of central Kashmir when he was arrested by the NIA on October 24 last year. He is currently in judicial custody. His bail plea was dismissed by the trial court in New Delhi on March 7.
The NIA charge sheet included punishment for unlawful activities, punishment for raising funds for terrorist act, punishment for conspiracy, punishment for being member of terrorist gang or organisation, punishment for holding proceeds of terrorism, membership of a terrorist organisation and support given to a terrorist organization, under sections of UAPA.
The final report also accused him of hatching a criminal conspiracy, punishable under section 120-B of Indian Penal Code.
The agency said the case was registered on the basis of information regarding funds from Pakistan being sent to Jammu and Kashmir through hawala channels via Delhi to spread terrorism.
The NIA had earlier alleged that the accused had links with proscribed terrorist organisations like Hizb-ul-Mujahideen.
The agency, which had in 2011 arrested several persons including one Ghulam Mohd Bhat with Rs 21.2 lakh, alleged that Yousuf was "one of the several Indian contacts of Bhat" who had been in touch with him for receiving money transfer codes.
It had alleged that Yousuf's involvement was found in collecting funds from a terrorist outfit in Saudi Arabia as well as from other accused on the directions of his father, Mohd Yousuf Shah alias Syed Salahuddin, the self-styled supreme commander of the Hizb-Ul-Mujahideen.
Syed Salahuddin was declared a Specially Designated Global Terrorist by the US Department of State in June last year.
The NIA had registered two other cases related to terror funding -- one in November 2011 and the other in May 2017. It had filed a charge sheet against 10 people including Salahuddin in the April 2011 case.
In the latest case, the NIA arrested various people including some close relatives and aides of separatist leader Syed Ali Shah Geelani.