The new discoveries Monday bring the death toll from the eruption to at least 36. Rescue workers then called off the search for the day because of rising levels of toxic fumes.
Hundreds of Japanese police and military troops ascended the ash-covered slopes of Mount Ontake Sunday, searching for survivors and casualties from the eruption.
Officials say one person was rescued and other hikers were seriously injured.
Hundreds of people were stranded on the peak after it erupted Saturday without warning around noon, local time. Most made their way down Saturday evening.
Mount Ontake is popular among hikers in the autumn. The volcano, which sits on the border of Nagano and Gifu prefectures west of Tokyo, had its last major eruption in 1979.
One climber told NHK the eruption began with loud booms that sounded like thunder. Then came the ash, which surrounded the stunned hikers in darkness.
The meteorological agency has warned people to stay away from the mountain, saying hot debris could fall within a four-kilometer radius.