Seventeen people died when their homes collapsed and 15 drowned, while 44 were injured, according to the latest figures from the civil protection services seen by AFP.
The hardest-hit regions include Zinder in the south, Diffa in the southeast and Tillabery in the southwest. The capital Niamey has so far been spared.
The rains have damaged or destroyed more than 7,000 homes, collapsing classrooms, health centers, granaries and shops.
The rainy season, which runs from June to August or September, has become deadlier in recent years, including in the country's desert north.
Last year, at least 70 people died across the country and more than 200,000 were affected, according to local and UN figures.
"On average Niger loses 40 billion CFA francs ($63 million)... due to floods and droughts" each year, said Laouan Magagi, Niger's minister for disaster management.
Niger, the world's poorest country by the benchmark of the UN's Human Development Index, is often hit by floods when badly needed rains arrive.