Witnesses heard a “thunder-like” boom before the eruption at the 3,067m (10,120ft) peak, situated between Nagano and Gifu prefectures.
PM Shinzo Abe says the army will help rescue some 150 climbers sheltering in lodges near the summit.
Officials have warned residents within a 4km radius of the risk of debris.
Mount Ontake last erupted in 2007.
Some climbers have managed to descend.
Two of those injured have fractured bones caused by flying rocks, NHK said.
Three people are missing, believed buried under volcanic ash, it said. A fourth was rescued but remains unconscious, the broadcaster added, citing police.
Kiso Prefectural Hospital, near the mountain, said it had dispatched a medical emergency team.
“We expect a lot of injured people so we are now getting ready for their arrival,” said an official at the hospital.
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