Six people are believed to be buried under ash and dozens injured.
Columns of thick white steam were rising from the 3067 metre Mount Ontake, which erupted around noon on Saturday, spewing ash, rocks and steam on a sunny northern autumn weekend busy with tourists and hikers.
Seven people were unconscious and buried under ash, national broadcaster NHK said.
One was rescued but the others remained on the mountain, NHK said, and 42 people were believed to be injured.
Local media reported on Saturday that one person had died, but firefighters said the death had not been confirmed.
Japan's volcano Ontake erupts in Nagano prefecture, central Japan.
A suffocating blanket of ash up to 20 centimetres deep covered a large area of the volcano, trapping climbers and forcing up to 150 people to seek refuge.
Local officials believe close to 50 hikers sheltered overnight in cabins on the popular mountain.
One group of 23 hikers spent the night in a cabin and on Sunday were able to climb down to the start of a trail leading to the summit.
A Self Defence Force helicopter rescued a man and a woman near the summit, according to a spokesman at Otaki village in Nagano prefecture.
"The helicopter flew over there very early in the morning to survey the condition. Then it found the two people waving at it," a spokesman told AFP.
"Originally, the rescuers thought it might be difficult to go near them because ashes could rise (and damage the helicopter), but the conditions were better than they believed and they were able to rescue the two people," he said.
The two could walk unassisted, but were taken to hospital for observation, the spokesman said.
Some 230 hikers made it to safe ground on Saturday after the eruption.
Arial television footage showed a line of rescue workers, wearing orange uniforms or green camouflage, scaling ash-covered trails on Sunday.
Some of the injured were hit by flying rocks or suffered burns after inhaling hot volcanic ash, the Yomiuri Shimbun newspaper said.
The meteorological agency forecast further eruptions, warning that volcanic debris might land as far away as four kilometres.
The last significant eruption of Mount Ontake, which lies in the centre of the main island, was in 1979 when it expelled more than 200,000 tonnes of ash, according to local media.
A more moderate eruption occurred in March 2007.
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