The fire and disaster management agency has raised the alert level for the island to five, its highest level. But officials say there is no threat to human life.
Nevertheless, the eruption was big news, and Prime Minister Shinzo Abe appeared on television to pledge that he had mobilised "all functions of government" to ensure the islanders' safety.
Volcano experts have warned that more eruptions on a similar scale could follow.
Japan sits at the junction of several tectonic plates and is one of the world's most seismically active countries.
Some have linked an surge in recent volcanic activity to the devastating earthquake that struck on 11 March 2011, triggering a massive tsunami.
In September last year, Mount Ontake in central Japan erupted unexpectedly, killing dozens of hikers.