Khumlo Abi Anal of the separatist National Socialist Council of Nagaland has been held in what is the first arrest in the case, the National Investigation Agency (NIA) said.
The ambush occurred last month near the border with Myanmar in Manipur state.
Indian army attacked rebel camps inside Myanmar days after the attack.
Indian authorities said at the time that troops had destroyed two rebel camps in Myanmar and "returned safely", but Myanmar denied the reports.
The NIA said in a statement that  "investigation has revealed that the accused [Khumlo Abi Anal] was extensively involved in the conspiracy to attack the army personnel".
Last month's attack took place in the state's Chandel district, close to the border with Myanmar.
Police said rebels used rocket-propelled grenades and assault rifles to target the soldiers.
There has been a fresh surge in attacks on Indian troops along the border with Myanmar after a number of rebel groups joined hands and formed a new coalition in India's restive north-east.
Manipur has been relatively peaceful in recent years and the attack took authorities by surprise.
Along with other north-east Indian states, Manipur is poorly developed and has long complained of neglect by the federal government, fuelling unrest, correspondents say.
India says it has arrested a rebel leader in connection with the killings of 20 of its soldiers in an ambush on a troop convoy in north-east India.