Davinder Singh, posted as the deputy superintendent of police, was arrested last weekend along with Naveed Babu, self-styled district commander of banned Hizbul Mujahideen, a new recruit Atif and an advocate Irfan Mir.
The four were caught with arms and ammunition while they were travelling in a car near Qazigund on the national highway in south Kashmir.
After receiving orders from the Union Home Ministry, the NIA has re-registered this case and started the investigation, the spokesman said.
Watch | Davinder Singh case: NIA takes over the investigation