Although there were no reports of injuries or damage, the authorities have decided to evacuate some 150 residents of the small island, NHK national television reports.
Mount Shindake suddenly erupted about 10:00am local time, sending a large plume of black smoke some 9,000 metresinto the sky. The Japan Meteorological Agency has issued a level five warning for the area, the highest on its scale, advising evacuations.
A pyroclastic flow of gas and rock flowed down Mount Shindake and reached the ocean, according to authorities, who warn of the possibly of further large-scale eruptions and call for "extreme caution."
A Coast Guard ship was sent to the island for the evacuation of residents, and a military helicopter was also dispatched.
Japan's Chief Cabinet Secretary Yoshihide Suga said the government was making its utmost efforts to gather information and secure the safety of residents, emphasizing there was no risk to human life, according to Reuters.
The remote island is located fairly far away from any heavily populated urban areas and is located about 160km to the south of the Sendai nuclear plant, on Japan's southernmost main island of Kyushu. There were no reports of any irregularities at the plant following the volcanic activity.
As a precaution, some flights to Okinawa and Southeast Asia have been diverted.