NCP spokesperson and state Minority Affairs Minister Nawab Malik described the decision as a "cover-up" by the Centre to hide the wrongdoings of the previous BJP-led government in the state.
A bench of Justices R F Nariman and S Ravindra Bhat issued notice to the Centre and sought its reply within four weeks.
The four were caught with arms and ammunition while they were travelling in a car near Qazigund on the national highway in south Kashmir.
Home Minister Amit Shah and Congress MP Abhishek Manu Singhvi accuse each other's govts of playing politics on Samjhauta bomb blast issue
Home Minister Amit Shah said Parliament should speak in one voice in giving powers to the NIA to send out a message to terrorists and the world
Separate bills will be introduced in Parliament in the coming days to amend the National Investigation Agency (NIA) Act and the Unlawful Activities (Prevention) Act, sources said
The agency also recovered Rs 750,000 in cash, 100 alarm clocks to be used as timer devices for bombs and 25 kilograms of bomb making ingredients
Two policemen of the Jammu and Kashmir Police were killed by Jhatt and his accomplice during their escape
The searches were conducted in Srinagar, Jammu and Gurgaon
The agency filed the charge sheet before District Judge Amar Nath against Naser Packeer, who was arrested in December last year
Like CBI, NIA's independence is open to question