© AFPNiger's capital, Niamey has seen heavy rains since June
The UN Office for the Coordination of Humanitarian Affairs (OCHA) said most of the deaths took place in the capital Niamey and that more than 11 000 homes were destroyed.
Niamey has been hardest hit along with Dosso in the south, Tillaberi in the west and the central-southern areas of Maradi and Zinder as Niger struggles once more with flooding which claimed more than 50 lives last year.
The recovery from the disastrous rains promises to be long.
Food production will also take a hit, with the flooding killing some 16 000 cattle and about 12 000 hectares of crops being ruined, the UN said.
With its 17 million population in a country three quarters of which comprises desert, Niger regularly is beset by food shortages caused by drought as well as severe flooding.
A humanitarian source told AFP on Thursday that exacerbating the problems were rising River Niger water levels, leading to fears of a repeat of serious flooding in 2012 which left dozens dead and some 500 000 homeless.
Last week, Niger said it had launched a campaign to destroy mosquito breeding sites to help combat the spread of deadly malaria in Niamey after the rain transformed some areas into swamps.
Comment: "This year's rain is just extraordinary," Katiellou Lawan Gaptia, head of meteorology at Niger's Met Office said. "In Niamey alone, the season's rainfall has increased by 84 percent since 2010."