The 48-hour-long Pampore encounter ended on Monday afternoon with the death of three militants, police said.
An official said that a mopping up operation is in progress to sanitise the multi-storey building.
The gunfight started on Saturday evening when militants attacked a CRPF bus at Sempora (Pampore) on the Srinagar-Jammu highway.
After attacking the bus, the militants had entered the JKEDI complex and taken cover in the multi-storeyed building.
Six people, including two captains and a soldier of Para 9, two paramilitary troopers of the Central Reserve Police Force (CRPF) and a civilian had earlier died in the gunfight.
The slain people include Abdul Gani Mir of Gundipora Pulwama, JKEDI gardener, captain Pawan Kumar of 10 para regiment belonging to Jind (Haryana), captain Tushar Mahajan of nine para regiment belonging to Udhampur town of Jammu region, Lance naik Om Prakash of nine para regiment, head constable Bhola Prasad and driver constable R. K. Rana, both of the CRPF.
More than a dozen other troopers have been injured in the twin-attacks.