It was the first time the weather agency issued an eruption warning since it began using a new bulletin system in August. The immediate eruption warning is issued to help locals and climbers evacuate from the area more quickly.
The weather agency also upgraded the alert level from 2 to 3, which prohibits people from entering the mountain.
As of about 10 a.m., there had been no reports of casualties, Kumamoto Prefecture said.
Japan lies on the “Ring of Fire” — a horseshoe-shaped band of fault lines and volcanoes around the edges of the Pacific Ocean — and is home to more than 100 active volcanoes.
Last year, Mount Ontake, which straddles Gifu and Nagano prefectures, erupted unexpectedly, killing 63 — the nation’s worst volcanic disaster in nearly 90 years. In May, Kuchinoerabu Island, a remote islet off Kagoshima Prefecture, was evacuated after an eruption there.