District official Khimananda Bhusal told AFP on Friday that the buses were carrying at least 66 people between them, but three passengers had been able to escape and were treated at a local hospital.
The accident happened before dawn along the Narayanghat-Mugling highway, around 100km 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.
The rainfall is hard to forecast and varies considerably, but scientists say climate change is making the monsoon stronger and more erratic.
Floods, landslides and lightning strikes have killed 88 people across the country since the monsoon began in June, according to police figures.
