"A detachment of security forces was attacked northwest of Tapatol by more than a hundred terrorists," the ministry said in a statement broadcast on national television.
The statement added that the attack saw "the use of improvised explosive devices and suicide vehicles".
According to the statement, "the attack resulted in the death of 29 soldiers and it was decided to declare national mourning for them for three days."
Niger's defence ministry said on Wednesday that at least 12 Nigerian soldiers had been killed after hundreds of armed rebels attacked motorcycles in the southwest.
The Defense Ministry statement said seven soldiers died in combat while five others were killed in an accident while driving to reinforce the unit that was attacked.
The attack took place in Kandaji, about 190 km from the capital Niamey, near the tri-border region of Mali, Burkina Faso and Niger, which has been a hub for extremists in the Sahel region for the past few years.