There were no immediate reports of injuries and damage as of late Sunday morning, according to the Toshima Village website on the island.
The Japan Meteorological Agency urged those in the area to "refrain from entering the danger zone".
Mount Otake spewed rocks to areas beyond its one-kilometre radius, the agency said.
The village authorities warned residents of possible future eruptions that may send large rocks in the air and to the surrounding area.
Japan sits on the Pacific Ring of Fire, an arc of intense seismic and volcanic activity that stretches through Southeast Asia and across the Pacific basin.
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