The force of Friday's landslide in central Chitwan district pushed the vehicles over concrete crash barriers and down a steep embankment, at least 30 metres (100 feet) from the road.
"One body has been found about 55 kilometres (35 miles) from the accident site," police spokesman Kumar Neupane told AFP.
District official Khimananda Bhusal told AFP that roughly 50 people remained unaccounted for, revising down the number of missing from the 63 reported by authorities on Friday.
"It is hard to confirm the total number because we don't know if the buses stopped to add or remove passengers along the way," he said.
Dozens of rescuers spent hours struggling to comb the raging Trishuli river with rafts, sensor equipment and dive teams to find any trace of the passengers or the vehicles.
Fierce currents made worse by this week's torrential downpours have hampered their efforts so far.
"We will employ all our abilities for search and rescue despite the water levels, current and the water's muddiness," Chitwan district chief Indra Dev Yadav told AFP.
The accident happened before dawn on Friday along the Narayanghat-Mugling highway, around 100 kilometres (60 miles) west of Kathmandu.
One bus was heading from the capital to Gaur in Rautahat district in southern Nepal, and the other was en route to Kathmandu from southern Birgunj.
A driver was killed in a separate accident on the same road after a boulder hit his bus. He died as he was being treated at a hospital.
Deadly crashes are common in the Himalayan republic because of poorly constructed roads, badly maintained vehicles and reckless driving.
Nearly 2,400 people lost their lives on Nepal's roads in the 12 months to April, according to government figures.
Twelve people were killed and 24 injured in an accident in January when a bus heading to Kathmandu from Nepalgunj fell into a river.
Road travel becomes deadlier during the annual monsoon season as rains trigger landslides and floods across the mountainous country.
Monsoon rains across South Asia from June to September offer respite from the summer heat and are crucial to replenishing water supplies, but also bring widespread death and destruction.
Floods, landslides and lightning strikes have killed 88 people across the country since the monsoon began in June, according to police figures.
