Rain has been pouring down since Friday night and is expected to continue over the weekend.
Home Ministry spokesperson Rishiram Tiwari told reporters there were 66 people reported dead across the country, of whom 34 were in the capital, Kathmandu.
Sixty people were injured and 3010 rescued across the Himalayan nation, he added.
He said all divisions of security forces in the country including the army have been ordered to help in the rescue efforts.
Several roads were blocked by landslides triggered by the rainfall.
Three highways, including the key Prithvi highway, connecting Kathmandu to the rest of the country have been blocked by landslides, and heavy equipment is being used to try open the routes, said Tiwari.
The government had issued flood warnings across the Himalayan nation warning of massive rainfall.
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 are 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.
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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.
Most of Kathmandu was without power and internet for a period of time.
The monsoon season that bringS heavy rainfall began in June and usually ends by mid-September.