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The eruption of the 1,117-metre (3,665-foot) Mount Sakurajima near Kagoshima city took place around 4:30 pm (0730 GMT), Jiji Press said.
A large amount of volcanic ash fell in the northern and central parts of the city, causing a delay in train services and temporary poor visibility, forcing car drivers to use their headlights.
The eruption also resulted in a small flow of volcanic material up to about one kilometre (half a mile) from the crater, Jiji said.
It was the 500th eruption this year of Sakurajima, which is about 950 kilometres southwest of Tokyo. The eruption lasted for about 50 minutes.