The weather improved on Sunday following three days of monsoon rains, and rescue and clean-up efforts were under way.
Kathmandu remained cut off as three highways out of the city were blocked by landslides.
Rescuers retrieved 14 bodies on Saturday night and Sunday morning from two buses that were headed to Kathmandu when a landslide buried them.
Another 23 bodies were dug out from vehicles on Sunday on the same spot, about 16 kilometres rom Kathmandu, and workers searched for others who may have been buried.
A statement by the Nepal police said another 86 people were injured in the flooding and landslides while 62 are missing.
The death toll was expected to rise as reports come in from villages across the mountainous country.
Residents in the southern part of Kathmandu, which was inundated on Saturday, were cleaning up houses as water levels began to recede.
At least 34 people were killed in Kathmandu, which was the hardest hit by flooding.
Police and soldiers were assisting with rescue efforts, while heavy equipment was used to clear the landslides from the roads.
The government announced it was closing schools and colleges across Nepal for the next three days.
Earlier on the weekend, Home Ministry spokesperson Rishiram Tiwari said all divisions of security forces in the country including the army had been ordered to help in the rescue efforts.
The government had issued flood warnings across the Himalayan nation warning of massive rainfall ahead of the downpour beginning on Friday.
Buses were banned from traveling at night on highways and cars were discouraged. Security forces were ordered to high alert.
Home Minister Ramesh Lekhak told reporters that officials were still collecting information on the effects of the flooding.
“The government’s priority right now is to rescue the people and help those who have been affected,” Lekhak said.
Parts of Kathmandu were inundated by swollen rivers with many houses flooded and residents forced to move to top floors.
A huge area on the southern side of the city was mostly flooded. An army helicopter was used to pick up four people who were unable to leave their houses.
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Most of Kathmandu was without power and internet for a period of time.
The monsoon season that bring heavy rainfall began in June and usually ends by mid-September.