The agency said on its website that Sakurajima in southern Kagoshima prefecture erupted at 6:56 pm (0956 GMT). There were no immediate reports of damage or injuries.
The eruption shot out large rocks, with the agency warning debris and pyroclastic flows — super hot and fast-moving mixture of gases and rock fragments — could reach as far as two kilometres (1.25 miles) away from the eruption vents.
The agency raised volcano’s alert status to Level 3, which bans entry onto the mountain, from Level 2, which limited people from going near the vents.
The elevated level stopped short of urging local residents to prepare for possible evacuation, according to the agency.
Local police have received no immediate report of damage on the peninsula of Sakurajima, where the volcano is located, which has a population of about 4,000 people.