The Makalu Air flight lost contact moments after takeoff and crashed into a hillside not far from its destination in the remote northwestern district of Humla.
The wreckage was found scattered across a mountain at an altitude of 3,900 metres (12,800 feet).
"Bodies of both the pilot and co-pilot have been recovered from the crash site," district chief Madhav Prasad Dhungana told AFP.
"We believe it missed the route and crashed into a hillside, probably because of bad weather."
Nepal has a poor road network and many remote mountain communities rely on planes and helicopters to bring in basic goods.
Nepal-based airlines are banned from flying in European Union airspace because of safety concerns.
In March, 51 people were killed when a passenger plane from Bangladesh crashed at Kathmandu airport, the country's deadliest accident in more than two decades.
Last month a Malaysian jet carrying 139 people aborted a takeoff and skidded into a muddy verge at the same airport, causing chaos and long delays. No one was hurt.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)
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