Rescuers in Nepal are struggling to recover bodies after monsoon rains swept away houses, killing dozens of people and sparking fears of a deadly cholera outbreak, officials say.

Three days of incessant rain have led to multiple landslides and flooding, killing at least 85 people and leaving more than 100 others unaccounted for, according to Nepal's Home Ministry.

The rains have damaged roads across the country's western plains bordering India, forcing officials to rely on helicopters to rescue stranded people as well as deliver emergency supplies.

Monsoon rains also forced officials to close a major bridge along the country's longest highway after it developed cracks and caved in.

As the weather cleared up late on Saturday, army officials evacuated thousands from the badly-hit Bardiya district in the country's western plains, Home Ministry spokesman Laxmi Prasad Dhakal said.

"We have evacuated 18,200 people in Bardiya and moved them to relief centres where they can get help," he told AFP.

"Our main worry now is of a possible cholera outbreak among the affected people.

"We have not seen any cases yet, but the health ministry has established camps to prevent any epidemic."

Cholera, which causes severe diarrhoea, vomiting and dehydration, is spread by eating or drinking food or water contaminated with human faeces.

As water levels slowly recede, rescuers have started moving out people out from their damaged homes into temporary shelters, national disaster management chief Yadav Prasad Koirala said.

"We are working hard to find the missing 113 people. Our choppers have been running sorties but it's a struggle," Mr Koirala told AFP.

The deaths come two weeks after the worst landslide in over a decade smashed into hamlets in north-eastern Nepal, killing 156 people.

Meanwhile, heavy downpours in neighbouring India have claimed at least 24 lives since Friday in northern Uttarakhand state.

Hundreds of people die every year in floods and landslides during the monsoon season in South Asia.

AFP