Not less than six militants had been killed within the raid on Friday, the ministry mentioned in an announcement on Saturday.
The insurgents attacked Diffa within the late afternoon, using in about 15 autos. After intense combating, they had been pushed again by safety forces,
The Boko Haram insurgency broke out in northeastern Nigeria in 2000, however violence continuously spills over into neighbouring Chad, Niger and Cameroon.
In December, an assault blamed on Boko Haram killed 28 individuals and burned 800 properties in Diffa area.