"From January 1 to March 29, 2015, some 345 cases of meningitis, including 45 fatalities, have been reported, which is a fatality rate of 15.3 per cent," the minister, Mano Aghali, said.
The capital Niamey is one of the hardest hit areas, with 18 deaths among 119 cases, while neighbouring Dosso has seen 18 deaths from 157 cases, Aghali said. All regions, except Diffa in the southeast, have seen cases.
But "the situation is under control," he told AFP.
Niger, one of the world's poorest countries, is frequently prone to meningitis epidemics.
The disease - an inflammation of the lining around the brain and spinal cord - can cause death within hours. It is usually bacterial or viral and occasionally is due to fungal infections, although almost any microbe can cause it.