The accused, Abid Ahmad Mir of Putrigam in south Kashmir's Pulwama, is alleged to be an overground worker of the banned Jaish-e-Mohammed terror outfit.
"They were arrested in a late-night operation from Kokernag on Saturday and are being questioned," an official said.
A team of the NIA had visited the encounter site on Friday evening and the federal agency is likely to take over the case for a thorough investigation, they said.
A CISF officer was also killed in the gunfight, while four security men were injured.
“We have recovered two AK rifles, a few satellite phones and other documents from possession of the slain militants. The search operation was going on,” the ADGP said.
Among the slain militants is top Lashkar-e-Toiba commander Yousuf Kantroo, who was the longest surviving LeT militant and had been active since 2020.