Issuing a statement following an emergency meeting on Sunday, the human rights watchdog appealed the Nepal government, security agencies, national and global organizations to expedite the rescue and relief operation in flood and landslide affected settlements.
Local officials have opened temporary shelters for displaced people in schools or public buildings.
The country's home ministry said on Sunday that the death toll had risen to 49, with 17 people injured and thousands left homeless.
Home Minister Janardan Sharma on Sunday visited the flood affected areas to review the situation.
An official said torrential rain, landslides and flooding have killed dozens of people in Nepal over the past three days, washing away hundreds of homes and damaging roads and bridges across the Himalayan country.
1005 houses have been damaged and more than 30,000 houses are inundated.
Many highways have been obstructed and the government has mobilised security forces and government officials to start search and rescue operations as well as rehabilitation works promptly.
Nepal's National News Agency reported Sunday that 600 tourists, including 400 foreigners, are trapped in the town of Sauraha in southwestern Nepal. Other roads remain blocked by the landslides, slowing down the rescue efforts.
The District Natural Disaster Rescue Committee has distributed dry foods to victims in the flood-hit areas.
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.
Monsoon rains, which start in June and continue through to September, are important for farm-dependent Nepal, but they also cause havoc each year.