The Disaster Management Department of the Japanese Ministry of Internal Affairs and Communications said that as of 8:30 a.m. (00:30 GMT), 13 people had been injured in the prefectures of Miyazaki, Kagoshima and Kumamoto on the southern island of Kyushu due to falls or being struck by objects.
In the city of Nichinan in the Miyazaki region, the earthquake caused the roof of a gymnasium to collapse, which had been designated as an evacuation shelter and is expected to remain closed.
The quake struck at 4:43 p.m. Thursday (08:43 GMT) at a depth of 30 kilometers in the Hyuga Sea, off the coast of Miyazaki, according to data from the Japan Meteorological Agency (JMA).
The JMA has issued a tsunami warning, with a half-metre-high wave hitting the Pacific coast of southwestern Japan.
Nuclear plant operators have not reported any anomalies or damage to reactors at the Sendai plant in Kagoshima and the Ikata plant in Ehime.
Experts have warned of the possibility of aftershocks in the coming days, and the JMA said Thursday's quake appears to be linked to a larger earthquake on the Nankai Fault, one of the world's most active seismic hotspots and where a major earthquake is expected to occur in the coming decades.
In response to the warning, JR Central railway company announced it would reduce train speeds on the Tokaido high-speed train line between Mishima and Mikawa.
The quake occurred days before the start of the Buddhist Obon festival holiday period, celebrated this year from 13 to 16 August to honour deceased ancestors.
Japan is located on the so-called Pacific "Ring of Fire" and experiences earthquakes relatively frequently, so its infrastructure is specially designed to withstand tremors.
