Torrential rain last week triggered multiple landslides and flooding, devastating entire villages, stranding thousands and damaging roads across the country's western plains bordering India.
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.
Dhakal said rescuers were still searching for 126 people reported missing.
As water levels gradually recede, allowing rescue workers to use land routes instead of relying entirely on helicopters, thousands of people have been evacuated into temporary shelters.
In the worst-affected districts of Surkhet, Bardiya and Dang, officials scrambled to provide clean drinking water kits to distraught villagers amid fears of a cholera outbreak.
"We are concerned about water-borne diseases spreading, especially cholera, and have deployed health personnel to distribute water purification tablets and medicines," Dhakal said.
Cholera is a potentially deadly disease spread by eating or drinking food or water contaminated by human faeces.
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.
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