The agency made the announcement Monday as Nigeria's annual rainy season is coming to an end. The report covered July through the end of October.
The agency said Adamawa and Kogi state suffered the worst casualties, with more than 18,000 people being injured.
Heavy seasonal rains typically cause flooding across Nigeria, as drainage can be poor in areas and people live in floodplains. However, the flooding this year was exacerbated by heavier than normal rains that cause officials in both Nigeria and neighboring Cameroon to open strained dams.