Earlier army had put the death toll at 30.
Saad Bello of the National Emergency Management Agency (NEMA) in Adamawa state said, "From our updated records we have 45 dead and 33 injured in the twin suicide bomb explosions in Madagali."
There was no immediate claim of responsibility, yet the blasts bore_ all the hallmarks of Boko Haram, which regularly uses women and young girls to carry out suicide attacks in its seven-year insurgent campaign in the troubled region.
Earlier Military spokesman Badare Akintoye had said "at least 30 people have been killed in the suicide blasts carried out by two female suicide bombers in the market."
According to a local government official and the National Emergency Management Agency (NEMA) confirmed the attack.
The chairman of Madagali local government Yusuf Muhammad said, "The two bombers who (were) disguised as customers, detonated their suicide belts at the section of the market selling grains and second-hand clothing."
The blitz on Madagali, which was evoked by Nigerian forces from Boko Haram jihadists in 2015, was the third time the town has been targeted since December last year when two female suicide bombers killed scores.
"Friday's blasts happened around 9:30 am (0830 GMT), it was dead bodies and wounded people in the midst of blood, spilt grain and abandoned personal effects," Market trader Habu Ahmad said.
NEMA spokesman for the northeast Ibrahim Abdulkadir said that the rescue teams had been deployed to the scene.
The spokesman further said that the security agents had cordoned off the scene of the explosions.
President of Nigerian Muhammadu Buhari condemned the attack in a statement on Friday , vowing to put "an end to this senseless loss of innocent lives."
Muhammadu Buhari said "This latest attack is obviously an act of desperation, but the Nigerian military will neither be distracted nor relent,".
President urged Nigerians to be more vigilant and immediately report any suspicious activity to the nearest security agents.
"The battle against terrorism is a joint effort involving all citizens, both government and governed."
He added "together, Nigerians can and will defeat the evil that is Boko Haram".
The situation in the region was "under control", Buhari had told a security conference in Senegal on Wednesday.
Boko Haram is seeking to impose a hardline Islamic legal system on Nigeria´s mainly-Muslim north. Its campaign of violence has killed at least 20,000 people and displaced some 2.6 million since 2009.
Anti-Jihadists campaign of Nigeria´s military is increasingly bogged down as it confronts suicide attacks, looting and indiscriminate slaughter.
The United Nations (UN) has warned that the affected region faces the "largest crisis in Africa".
The UN evaluates that 14 million people will need external help in 2017 because of the unending violence, particularly in Borno State, the epicentre of the rebellion.