The quake occurred at 17:05 GMT, with an epicenter 580 kilometres (360 miles) south of Tokyo at a 19-kilometre (12-mile) depth, according to the EMSC website.
No casualties and damage have been reported.
In July, a 6.3-magnitude earthquake hit near the south coast of the Japanese island of Honshu, according to the European-Mediterranean Seismological Centre.
Earlier in the month, a 6.1 magnitude earthquake hit off the Naze area of Japan's Kagoshima Prefecture, the US Geological Survey (USGS) said.
Japan is located in a seismically active zone known as the Ring of Fire and regularly suffers from powerful earthquakes. In 2011, a 9.0 magnitude earthquake and the following tsunami killed over 15,000 people and caused the Fukushima nuclear plant disaster.