The weather has destroyed more than 4,500 homes and more than 250 acres (100 hectares) of fields and gardens, according to data from the UN's Office for the Coordination of Humanitarian Affairs (OCHA) in Niamey.
The figures are sharply higher than the last UN estimates on August 12, which said 12 people had died and 27,000 had been affected by the flooding.
Floods are an annual problem in Niger as seasonal rains often cause streams and rivers to burst their banks, sweeping away homes and destroying crops.
Most of the country has been hit by the floods, with the exception of the eastern desert region, home to more than 80,000 refugees who have fled violence in neighbouring Nigeria.
The government launched an appeal for aid in mid-August for those affected by the rising waters.
In 2012, floods in Niger killed dozens of people and affected some 500,000 more, causing an estimated 148 million euros (USD 191 million) of damage, according to official figures.