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Health Minister Iliassou Mainassara said the operation will help combat the spread of deadly malaria in Niamey.
During a 20-day campaign which began on Thursday, spray guns mounted on pick-up vehicles will treat areas that have been transformed into swamps by flooding.
The liquid pesticide is not harmful to humans and animals, the minister said.
The floods have killed 41 people across Niger since June, according to the civil protection agency, after more than 50 deaths last year.
The operation is a joint exercise with Cuba, which pledged support for a malaria control programme across the country in 2014.
Malaria kills around 2,000 people, mainly children, every year in Niger and is responsible for around 80 percent of visits to doctors during the rainy season.
Of the more than two million malaria cases reported in 2015, 60 percent were children under five, according to health ministry figures.
To fight malaria, the country and its partners have so far focused on the free distribution of treated bed nets, which aid organisations say are largely responsible for a 25 percent drop in cases between 2005 and 2015.
There is no vaccine against malaria and efforts to stop the spread of the disease are often hampered by a lack of understanding among the population.
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