The earthquake struck at around 2 a.m. local time on Sunday (17:00 GMT) about 170 kilometers (105 miles) from the northeastern Japanese city of Miyako.
The epicenter was located at a depth of around 10 kilometers (6.2 miles), USGS added.
Minutes later, two magnitude 5.3 earthquakes were registered in the area at the same depth, according to USGS.
No victims or damages have been reported so far.
Japan is a seismically active region. In March 2011, a 9.0-magnitude offshore earthquake triggered a 46-foot tsunami that hit Japan's Fukushima nuclear power, leading to the leakage of radioactive materials and the shutdown of the plant. The accident is considered to be the world's worst nuclear disaster since Chernobyl.
According to the Richter scale, magnitude 6.0-6.9 quakes are considered strong and can cause moderate damage to even earthquake-resistant structures.