Aheto Chopey, a resident of Dimapur's Unity village, was arrested in a joint operation by the National Investigation Agency (NIA) with Assam Rifles, it said in a statement.
He was intercepted near Zubza area in Kohima.
A non-bailable arrest warrant was issued against him by an NIA court in Nagaland's Dimapur.
The officials have recovered one AK-56 rifle, two 9mm pistols along with magazines, assorted ammunition and Rs 1,32,000 in cash from his possession, it said.
The case, registered in 2013, relates to the supply of government arms and ammunition to Naga underground factions The National Socialist Council of Nagaland-Unification (NSCN- U) and National Socialist Council of Nagaland Khaplang (NSCN-K), the statement added.