A Home Ministry official said more than 5,000 people had been shifted from the affected areas.
Monsoon floods and landslides have killed at least 94 people across Nepal but officials fear that figure could rise sharply as rescuers search for dozens believed lost under mud and in submerged villages.
Five thousand and six hundred trained personnel of the Nepal Police, one thousand 700 APF personnel, and 8,300 Nepalese Army personnel, as well as helicopters, have been mobilized for search and rescue operation, the Ministry has stated.
"The toll may increase as we are still compiling the final tally", said an aide to Home Minister Janardan Sharma, Laxmi Pun, according to Reuters.
"Since Friday, at least 40 people have been killed in the floods and landslides", Home Ministry spokesman Deepak Kafle said.
The District Natural Disaster Rescue Committee in its emergency meeting estimated that around 50,000 people have been hugely affected as floodwaters destroyed foodstuff and other belongings.
9/11 victim identified 16 years on
However, 1,112 people - about 40 percent - who died on 9/11 still remain unidentified, according to the medical examiner's office. As DNA testing propelled, so has the multimillion-dollar push to interface more than 21,900 bits of stays to singular casualties.
There is criticism against India for not opening floodgates on the rivers on time, which has resulted in floods in southern Nepal, especially in the Terai region. "We are also providing relief to the victims".
Nepal's National News Agency reported Sunday that 600 tourists, including 400 foreigners, are trapped in the town of Sauraha in southwestern Nepal. "Hundreds of families are taking shelter in local schools", said Raghu Ram Mehta, a resident of Sunsari district, which has suffered nine deaths, the highest of any district.
In the eastern city of Biratnagar, the airport was closed after the runway was submerged under more than half a meter (2 feet) of water.
Prime Minister Sher Bahadur Deuba expressed his condolences and urged people to remain.
The weather forecasting office says more rain is expected on Sunday throughout the country.