The Japan Meteorological Agency said the quake was centred off the eastern coast of Japan's southern main island of Kyushu at a depth of about 30 kilometers.
It issued a tsunami advisory, predicting waves of up to 1 metre along the southern coast of Kyushu and the nearby island of Shikoku, Euro News reported.
The quake most strongly shook Nichinan city and nearby areas in Miyazaki prefecture on Kyushu island.
The agency said tsunami waves of up to 50 centimetres were detected along parts of Kyushu's southern coast and the nearby island of Shikoku about a half hour after the quake struck.
Seismologists were holding an emergency meeting to analyse whether the quake had affected the nearby Nankai Trough, the source of past devastating earthquakes.
Operators of nuclear plants in Kyushu and Shikoku said they were checking to see if there was any damage to them.
Japan’s NHK public television said there were reports of broken windows at the Miyazaki airport near the epicentre.
Japan, located within the Pacific "ring of fire," is considered one of the most earthquake-prone regions globally.
The Asian island country accounts for about 20% of global quakes of magnitude 6.0 or greater, with seismometers recording an event every five minutes on average, forcing the country to invest greatly in making its infrastructure and its population quake-resistant.
SD/pr