A senior military officer in Bama confirmed the death toll, adding that nine people were also injured in the bombings.
Media reports stated that the suspected militants, a man and a woman, detonated their explosives inside the mosque during morning prayers on Saturday in Borno state.
Bama local government chairman, Baba Shehu Gulumba said: "The pair blew themselves up in a mosque while people were praying, killing three people."
Boko Haram militants have wreaked terror in the region with attacks on civilian and military targets in response to army offensives that have put pressure on the Takifiri group.
On April 5, Borno State's information commissioner, Mohammed Bulama, said 1,200 people had returned to the town in a phased resettlement of the 100,000 displaced residents living in camps in Maiduguri.
