Meteorologists issued warnings after torrential rains hit the country's eastern and central regions on Friday.
"Hilly regions have been hit by landslides, while the eastern plains region has suffered inundation," said Umakanta Adhikari, an official at the Home Ministry.
Nepal has been lashed by heavy rains in the last three days.
The weather forecast division has warned of continuous rains and strong winds in several parts of the country over the weekend.
At least four highways in different parts of the country have been blocked by landslides, according to the National Emergency Operation Centre.
The monsoon in Nepal, which lasts from July to September, causes disastrous landslides and flooding every year, killing hundreds of people.