Low-lying neighbourhoods in Nepal's capital Kathmandu were inundated by surging floodwaters on Sunday after ferocious monsoon rains that police said had killed at least 101 people around the Himalayan republic.

Deadly rain-related floods and landslides are common across South Asia during the monsoon season from June to September, but experts say climate change is increasing their frequency and severity.

Large swathes of eastern and central Nepal have been inundated since Friday with flash floods reported in several rivers and extensive damage to the country's highways.

"The death toll has reached 101, and 64 people are missing," said police spokesperson Dan Bahadur Karki.

"There is likely to be an increase in the death toll as our search and rescue mission proceeds in the affected areas," he added.

The Kathmandu valley recorded 240 millimetres of rain in the 24 hours to Saturday morning, the country's weather bureau told the Kathmandu Post newspaper.

It was the highest rainfall recorded in the capital since at least 1970, the report said. (AFP)