The toll could go higher as three dozen people were reported missing. Another 17 were injured.
The heavy rain, which mainly hit the country's southern plains, led to the evacuation of 5,000 people, a Home Ministry official said.
More than 30 people were reported dead on Saturday.
Army and police personnnel continued search and rescue operations, with more than 34,000 houses submerged, the official added.
"The number of dead could increase as we are still compiling the final tally," said Laxmi Pun, an aide to Home Minister Janardan Sharma, told Reuters.
Monsoon rains which start in June and continue through September are important for farm-dependent Nepal, but they also cause havoc each year.
(Reporting by Gopal Sharmal Editing by Kim Coghill)
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