The statement on Thursday said most of the militants were killed by air strikes while 87 others were neutralized by ground troops last week.
According to the ministry, government troops involved in the operation suffered no casualty.
It claimed that eight boats belonging to the militants were destroyed and a large haul of equipment and other goods were commandeered, including three vehicles stolen on 22 November in Toumour, a locality in the region.
Mobile phones, machine guns, rocket propel launchers and several AK47-type individual weapons with 2,000 cartridges of all calibers were also recovered.
Among the hauls were pharmaceuticals, including psychotropic drugs, the ministry said.
The large-scale operation was undertaken as the Diffa region witnessed a resurgence in attacks ostensibly by Boko Haram fighters.
Recently questioned by the Chadian PMs on the issue, Defense Minister Kalla Moutari had warned that Boko Haram attacks on Niger would increase from January onwards, a period which he believed to be the beginning of the fall in the water levels of the Komadougou river which serves as a natural border between Niger and Nigeria.