The aircraft went missing shortly after taking off from the popular mountain resort town of Pokhara on October 8 with a Russian pilot and a South African tourist on board.
Search teams were dispatched to the area after debris was spotted from the air, Pokhara's airport chief Bhola Prasad Guragain told AFP.
"The team recovered wreckage of the ultralight craft and bones from the site," Guragain said. "The marks on the wreckage confirm it is the missing craft but we have handed the remains to authorities for tests."
In 2013, a Chinese tourist and a Nepali pilot were killed when their ultralight crashed in the same area.
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Nepal, which is still reeling from a devastating earthquake last April, has suffered a number of air disasters in recent years.
Most have been attributed to inexperienced pilots, poor management and inadequate maintenance.
The European Union blacklisted all Nepal's airlines in 2013.
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