No tsunami warning was issued after the quake struck with an epicentre 45 km (30 miles) deep at 1:08 a.m. (1608 GMT on Friday) off the coast of Kyushu, the southernmost of Japan's four main islands, the Japan Meteorological Agency (JMA) said.
The quake caused shaking in Oita and Miyazaki prefectures that measured 5+ on Japan's seismic intensity scale, which has a maximum of 7, the agency said.
Thirteen people were injured in nearby regions, including two people in their 80s who were seriously hurt, the Yomiuri newspaper reported, citing local authorities.
Multiple reports of damage to buildings, water pipes and roads have been confirmed, said public broadcaster NHK.
No abnormalities were reported at the Ikata nuclear power plant, operated by Shikoku Electric Power, or the Sendai plant operated by Kyushu Electric Power in southern Japan, the Nuclear Regulation Authority said.
"In the past, 10% to 20% of strong earthquakes were followed by a quake of the same level, so be aware of another quake of up to 5+ intensity scale in regions that experienced large jolts, for around a week," the JMA said in a statement.
(Reporting by David Dolan and Kantaro Komiya; Editing by Catherine Evans and William Mallard)