Thomson Reuters
The man had helped the Islamist militant group plan several attacks, including the killing of traditional ruler the Emir of Gwoza, it said in a statement.
Two women were also arrested as part of the investigation, one of whom was accused of coordinating payments to other "operatives".
A year old intensive military operation against Boko Haram has so far failed to crush the rebels, whose struggle for an Islamic state in largely Muslim northern Nigeria has killed thousands since it was launched in 2009.
The insurgency has destabilized much of the northeast of Africa's top oil producer and biggest economy.
The abduction in mid-April of 276 school girls, 219 of which remain in captivity, has become a symbol of the government's powerlessness to protect civilians from attack.
Defense spokesman Major-General Chris Olukolade said in a statement that the arrested man used his membership of a pro-government vigilante group "as a cover, while remaining an active terrorist". Olukolade said the man had coordinated several deadly attacks in Maiduguri since 2011, including on customs and military locations as well as the planting improvised bombs.
Violence has been relentless in northeast Nigeria in particular, with hundreds killed in the past two months. There have also been bombings blamed on the militant group in the capital Abuja. On Sunday, the Chibok community was attacked again in three places. Militants opened fire on churches and homes, killing dozens and burning houses to the ground.
(Reporting by Lanre Ola Additional reporting by Camillus Eboh in Abuja; Writing by Tim Cocks Editing by Jeremy Gaunt)