"I am calling on all residents to evacuate the flood zones and immediately leave homes that are close to collapsing," the governor of the Niamey region, Soumana Ali Zataoua, said in a televised address.
Two people, a father and son, were killed Saturday when a wall collapsed, according to TV reports, after more than 100 millimetres (nearly four inches) of rain fell in just a few hours in the capital.
Many of the homes at risk are located in the former bed of the Gountou-Yena river, which is now once again filling with water, said Abdoulaye Bako, head of the national civil protection agency.
"Several neighbourhoods are being seriously threatened," he said.
In Gabagoura, a village to the west of Niamey, more than 300 homes have been destroyed and several people wounded, said village chief Amadou Souley.
"Go where? We lost our home, money and clothes," said Ramatou Ali, in his 70s, who lives in the village.
Municipal authorities say they have asked the affected residents to stay in schools.
Flooding has killed 41 people across Niger since June, according to the civil protection agency, after more than 50 deaths from flooding last year.
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