During interrogation, the cadres have admitted to carrying out extortion in the region.
The arrested militants have been identified as Nongman Jugli and Sampan Harap of NSCN (R) and Anil Kanikar and Pramod Barua of ULFA (I).
Extortion in south Arunachal Pradesh has been on the rise in the pre monsoon season.
Reports of various fractions of NSCN and ULFA (I) carrying out extortion activities in the region were received in the past few weeks.
Arms, ammunition and incriminating documents were recovered from the possession of the arrested militants.
Meanwhile, Assam Rifles reunited a 14-year-old minor girl, recruited by the United National Liberation Front (UNLF), also known as the United National Liberation Front of Manipur, with her family.
On receipt of specific information about the desertion of a minor girl cadre of UNLF from Thongren Camp in Myanmar and seeing her resolve, Assam Rifles swung into action to assist in freeing the minor girl from the clutches of the UNLF.
The Tulihal Battalion of the Assam Rifles in a joint operation with Bishenpur Commandos recovered huge cache of automatic weapons and other warlike stores in Pat area of Ishok Makha Leikai of Bishnupur district in Manipur.
The recoveries included two M16 rifles, four AK-56 rifles, one A4 rifle with UBGL.