In a statement read out on national television, Niger's cabinet said 32 people had died when their buildings collapsed, and another 32 drowned.
The floods and landslides had affected close to 70,000 people in total, the statement said, with more than 5,000 houses destroyed or damaged.
The worst-affected regions are Maradi in the south, Agadez in the Sahara desert, and the capital Niamey.
Cholera is spreading as a result, killing 16 people so far, the health ministry warned.
Niger's rainy season normally lasts three to four months, from June to August or September.
But it has been particularly deadly over the past few years, including in northern desert regions, in a country where crop failures are normally attributed to drought.
In 2020, floods caused 73 deaths and created a humanitarian crisis with 2.2 million people needing help, according to the United Nations.
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