The black cloud reached as high as 9,000 metres (29,500 feet), the agency said, and was accompanied by a five-minute volcanic quake.
Top government spokesman Yoshihide Suga said there were no reported injuries and that less than two hours after the eruption, most of the island’s 137 inhabitants had moved to an evacuation centre, where they were waiting for coastguard boats.
Television pictures showed the after-effects of the pyroclastic flow, which had cascaded down the mountainside towards one of the island’s harbours.
Grey ash blanketed the breakwaters and discoloured the sea.
Community leader Nobuaki Hayashi told NHK of how the eruption, which came around 10:00 am, had blocked out the morning light.
“Dark smoke rose quite high, I couldn’t tell how high. But it became dark outside,” he told the network.
Others spoke of “a big bang” when the volcano burst into life.
The volcano has been under observation since an eruption last year, with a two-kilometre (one-mile) exclusion zone in place, but volcanologists on Friday rapidly raised the alert level to five — the highest on the scale — triggering the evacuation order.
“A volcanic eruption occurred at Shindake at 9:59 am. Along with this eruption, a pyroclastic flow reached the coastline” of the island, the weather agency said.
Sadayuki Kitagawa, director of the volcanology division at the agency, warned the danger was not over.
“It’s possible that eruptions of a similar scale could happen in the future. We are warning residents about pyroclastic flows, and asking people to obey evacuation instructions,” he told a briefing.
Japan sits at the junction of several of the Earth’s tectonic plates and the country is dotted with active volcanoes.
Any eruption is big news, and sends the nation’s emergency response organs into a flurry of activity.
Prime Minister Shinzo Abe said he had mobilised “all functions of government” to ensure the safety of residents, including coastguard boats and military helicopters.
“I ordered authorities to swiftly gather information on damage, ensure local residents’ safety through evacuations, and boost observation of the volcano,” he told reporters.
Kagoshima prefecture, in which Kuchinoerabu sits, said it had requested the military send troops to help with disaster relief.
Major air carriers Japan Airlines and All Nippon Airways said there had been no immediate impact on flights.
Eruptions at Shindake have been recorded for nearly two centuries, with the last significant period of activity from 1966 to 1980.
Volcano expert Kazuhiro Ishihara, professor emeritus at Kyoto University, told NHK evacuation managers would be taking account of cinders and wind direction in deciding how to proceed.
“The eruption could continue for some time given the mountain’s history,” he said. – AFP