Another 126 people are missing after torrential rain last week triggered multiple landslides and flooding, devastating entire villages, stranding thousands and damaging roads across the country's western plains.
As the weather cleared Sunday after three days of incessant rain, the government deployed more than 3,400 workers and four helicopters to rescue stranded people and deliver emergency supplies, said Jhankanath Dhakal, chief of Nepal's National Emergency Operation Centre.
"We have found three more bodies this morning, bringing the total death toll to 101," Dhakal told AFP, adding that another body had been recovered overnight.
In the worst-hit districts of Surkhet, Bardiya and Dang, officials scrambled to provide clean drinking water kits to distraught villagers to try to avert a possible cholera outbreak.
"We have diagnosed a few cases displaying symptoms of cholera," said Tulashi Prasad Dahal, who is coordinating the health ministry's efforts to prevent an epidemic.
"People suffering from fever, dysentery, diarrhoea are being treated at nearby health posts: the problems arose because of impure drinking water and food," Dahal told AFP.
Cholera, a potentially deadly disease which causes severe diarrhoea, vomiting and dehydration, is contracted by consuming food or water contaminated by human faeces.
As water levels gradually recede, allowing rescue workers to use land routes instead of relying entirely on helicopters, thousands of people have been evacuated to temporary shelters.
In Surkhet district, which suffered the worst damage with roads still underwater, officials said workers were struggling to locate the 106 people reported missing.
Another 20 were reported missing elsewhere.
"The flood has destroyed our water pipes, our roads and cut off our electricity, making it difficult for us to carry out necessary search and rescue operations," district official Jagat Bahadur Basnet told AFP.
The deaths come two weeks after the worst landslide in more than a decade smashed into hamlets in the hilly northeast and killed 156 people.
Meanwhile, heavy rain in neighbouring India's Uttarakhand state has claimed at least 24 lives since Friday, reviving memories of a deluge last year that killed more than 5,000 people in the same region.
Hundreds die every year in floods and landslides during the monsoon season in South Asia.