A US-Bangla Airlines jet crashed as it was landing at the main airport in Kathmandu, breaking apart in a nearby field after it veered off the runway.
The flight, UBG 211, was en route to Kathmandu from Dhaka, Bangladesh.
Nepal army spokesman Brigadier General Gokul Bhandari said 50 people had died and the fate of the others was unknown.
But airport general manager Raj Kumar Chettri said the pilot disregarded their messages and came in from the wrong direction.
The aircraft received a green light to land in the southern area, but in the end it tried to do it in the north, he said.
Nepali authorities say the plane had an unusual landing while the airline says it was the air traffic control's fault.
The airport was temporarily closed for all worldwide flights following the accident.
"We will identify the dead tomorrow", he said.
According to the flight tracking website FlightRadar24, US-Bangla flight made a crashed landing at 14:20 local time (08:35 GMT).
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Numerous bodies on the tarmac were charred, witnesses said.
One survivor who managed to break through a window says the aircraft gave a violent shake, followed by a bang.
Dozens of firefighters and rescue workers responded to the site of the wreck, where scraps of the burned aircraft remained. "She gave a thumbs up, but I could see she was panicking", said Ashish Ranjit, 35, who escaped through a window on the plane's right.
Nepal has a poor road network and internal flights are key to accessing remote parts of the Himalayan nation.
The airport was shut for about three hours after the crash.
"Our team will fly to Nepal as soon as the airport is open", he added. There were 74 passengers on board but no casualties were reported.
The Bangladeshi carrier, which launched operations in July 2014 with a slogan - "Fly Fast-Fly Safe", operates Bombardier and Boeing BA.N aircraft.
There has been a series of accidents at Kathmandu's airport in the past.
Just two months earlier, a Thai Airways aircraft had crashed near the same airport, killing 113 people.
The 17-year-old plane had circled Tribhuvan International Airport twice as it waited for clearance to land, a company official said.