According to the Ministry of Home Affairs, at least 13 persons were injured in the rain-related incidents and 17 others remained missing.
Almost 600 tourists, including 200 Indians, have been stranded in central Nepal's popular tourist district Chitwan due to flooding triggered by heavy rains that have claimed 49 lives, officials said on Sunday.
Home Minister Janardan Sharma on Sunday visited the flood affected areas to review the situation.
"Since Friday, at least 40 people have been killed in the floods and landslides", Home Ministry spokesman Deepak Kafle said.
Some 36 people were missing in 23 districts across the country's densely populated southern plains, which border India.
More than 30 people were reported dead on Saturday.
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According to the ministry, some 35,843 houses have been inundated while 1,000 houses have been damaged in the low-lying areas known as Terai region of Nepal.
Nepal Police, Nepali Army and APF personnel are now performing rescue works in the state. Many roads are submerged or covered by debris from landslides, providing further challenges to rescue efforts.
A hotel owner said they used elephants to transport tourists to the nearest open highway and airport to help them return to the capital Kathmandu.
Meanwhile, Nepal Cabinet held an emergency meeting during which Prime Minister Sher Bahadur Deuba ordered the local district administrations to intensify the rescue and release activities.
The weather forecasting office says more rain is expected on Sunday throughout the country.
Heavy rains have been battering Nepal and northern India for days now, and the death toll from this year's monsoon season - which usually lasts from June until the end of August - has already exceeded that of 2016.