The agency also recovered a major cache of arms including assault rifles on the basis of his inputs.
Based on certain intelligence inputs, a joint operation was conducted with security forces, and Assam Rifles, near Village Tsiesena Basa, Kohima, the agency said.
"The operation led to the arrest of an accused Kisheto Ayem, at 14.30 hrs today, and one pistol with seven rounds was recovered from his possession," it said.
"All items have been seized. Grenade has been destroyed in situ by the security forces, and remnants seized. The accused is being produced before the NIA Special Court," the NIA said.
Four security personnel of the 19 Assam Rifles were injured on March 26 when suspected militants opened fire at the personnel who were waiting for a convoy from Cheswama near the Indira Gandhi (IG) Stadium.