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The capital Niamey has been hardest hit along with Dosso in the south, Tillaberi in the west and the central-southern areas of Maradi and Zinder, said the UN Office for the Coordination of Humanitarian Affairs (OCHA).
Twenty-one of the 50 fatalities were in the capital, while across the country 47 had been injured and some 117,600 displaced as of Monday by the flooding.
Flooding claimed more than 50 lives last year.
The recovery from the disastrous rains promises to be long, with some 9,000 dwellings and 31 schools destroyed.
Food production will also take a hit, with the flooding killing some 16,000 cattle and about 9,000 hectares (22,000 acres) 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 that exacerbating the problems were rising River Niger water levels over the past fortnight at Niamey, Dosso and Tillaberi, leading to fears of a repeat of serious flooding in 2012 which left dozens dead and some 500,000 homeless.
Despite the ongoing heavy rains, the Niger Basin Authority, coordinated by nine states in the region, said Thursday it saw a “downward trend” in water levels.
Even so, Niamey authorities called on civilians living in flood-hit areas to evacuate zones that are under threat.
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.
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