The search operation had only resumed earlier in the day after rescuers paused after dark on Sunday.
There were 19 passengers and three crew members on board the Twin Otter aircraft, operated by Nepali carrier Tara Air, airline spokesman Sudarshan Bartaula told AFP. The passengers included two Germans and four Indians, with the remainder Nepali.
Before the wreckage was found, Pokhara Airport spokesman Dev Raj Subedi told AFP early Monday morning that rescue helicopters and army troops on the ground had shifted their search to a suspected crash site.
“The search operation has resumed... There has not been any significant improvement in the weather. Two helicopters have flown toward the area but they have not been able to land yet,” he said.
Subedi said that they had followed GPS, mobile and satellite signals to the location.
The flight took off from the western town of Pokhara for Jomsom on Sunday at 9:55 am (0410 GMT), but air traffic control lost contact after 15 minutes, the airline said.
Jomsom is a popular trekking destination in the Himalayas about 20 minutes by plane from Pokhara, which lies 200 kilometres (120 miles) west of the capital Kathmandu.
Flight operator Tara Air is a subsidiary of Yeti Airlines, a privately owned domestic carrier that services many remote destinations across Nepal.
It suffered its last fatal accident in 2016 on the same route when a plane with 23 on board crashed into a mountainside in Myagdi district.
Nepal’s air industry has boomed in recent years, carrying goods and people between hard-to-reach areas as well as foreign trekkers and climbers. But it has long been plagued by poor safety due to insufficient training and maintenance.
The European Union has banned all Nepali airlines from its airspace over safety concerns.
The Himalayan country also has some of the world’s most remote and tricky runways, flanked by snow-capped peaks with approaches that pose a challenge even for accomplished pilots.
The weather can also change quickly in the mountains, creating treacherous flying conditions.