Floods and landslides triggered by heavy downpours in Nepal killed at least 59 people across the Himalayan country, with rescue teams searching for 44 missing, police said on Saturday.

Large swathes of Nepal have been inundated since Friday, prompting disaster authorities to warn of flash floods in multiple rivers.

"So far, there are 59 dead, 36 wounded and 44 missing," said Nepal police spokesman Dan Bahadur Karki.

Karki said more than 200 incidents of flood and landslides have been reported and that the toll was likely to increase further.

Rivers around the capital Kathmandu burst their banks, inundating nearby houses.

"It's scary. I had never seen such kind of devastation in my lifetime before," said Mahamad Shabuddin, 34, who runs a motorbike workshop in the city near the swollen Bagmati River.

Survivors were seen standing on top of buildings or wading through murky waters to get to safety.

"When I went outside in the middle of the night, the water had reached up to my shoulders," Hari Mallah, a 49-year-old truck driver said.

"My truck is completely under water."

Basanta Adhikari, a spokesman for Nepal's National Disaster Risk Reduction and Management Authority, said authorities were working to rescue and get relief to those impacted by the floods.

More than 3,000 security personnel were deployed to assist rescue efforts with helicopters and motorboats.

Rescue teams were using rafts to pull survivors to safety.

Landslides have blocked several highways, leaving hundreds of travellers stranded.

"We have around eight locations, all of them have been blocked due to landslides in different sections of the road," said Kathmandu traffic police officer Bishwaraj Khadka.

All domestic flights out of Kathmandu were cancelled from Friday evening, affecting more than 150 departures.

A landslide that hit a road in Chitwan district in July pushed two buses with 59 passengers aboard into a river.

Three people were able to escape alive, but authorities managed to recover only 20 bodies from the accident, with raging flood waters impeding the search.

More than 220 people have died in Nepal in rain-related disasters this year. (AFP)