"We appeal to all residents downstream (of the Niger River)... because the water keeps rising," the NBA's Soungalo Kone said late Saturday, speaking on Niger television.
The NBA has issued its second-highest alert level of orange, warning that further flooding is highly likely following months of heavy rain in Niger and Mali.
"It's a question of hours to get to a red alert -- the waters can rise very suddenly," said Lawan Magadji, Niger's minister of disaster management, speaking on local television.
Floods are threatening villages and some sections of the capital Niamey, the minister said.
The ministry has already announced plans to evacuate residents in affected areas and reinforce dykes.
The government has set up sites for people displaced by the flooding, the minister said.
Almost all Niamey's some million and a half residents live along the river banks.
Some of the homes at risk are located in the former bed of the Gountou-Yena river, which is now once again filling with water.
Flooding has killed 44 people across Niger since June, according to the civil protection agency, after more than 50 deaths from flooding last year.
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