One body was air-lifted by military helicopter, according to a crisis-management official at the Nagano prefectural government.
Public broadcaster NHK said another had been found, but there were no details on how far the recovery had got.
It is unknown whether the bodies are those of some of the 12 people unaccounted for.
A search operation involving some 1,000 police, troops and firefighters resumed early Tuesday after a two-day hiatus because of atrocious weather.
The 3,067 metre (10,121 feet) Mount Ontake erupted without warning on September 27, while it was packed with hikers.
Autopsies have revealed that walkers, many of whom had been enjoying lunch at the peak in the autumn sunshine, died largely from injuries caused by stones hurled out in the initial explosive eruption.