The quake hit at 11:39 am (0239 GMT) off the coast of Japan's main Honshu island, at a location about 350 kilometres (395 miles) southwest of Tokyo, USGS and the Japan Meteorological Agency said.
The quake was measured at a relatively shallow depth of 10 kilometres.
No damage or injuries were immediately reported though heavy shaking forced some of the country's bullet trains to temporarily stop running, public broadcaster NHK reported.
Japan sits at the junction of four tectonic plates and experiences around 20 percent of the world's most powerful earthquakes.
But rigid building codes and strict enforcement mean even powerful tremors frequently do little damage.
A massive undersea quake that hit in March 2011 sent a tsunami barrelling into Japan's northeast coast, leaving 18,500 people dead or missing, and sending several reactors into meltdown at the Fukushima nuclear plant in the worst atomic accident in a generation.