Officials said there were no immediate reports of major damage in the aftermath of the quake, though part of a temple wall collapsed in central Tokyo, injuring several people.
The quake, with its epicentre 80km below the surface in the Pacific Ocean east of Tokyo, struck at 03:55 GMT, the meteorological agency said.
Sitting atop the junction of at least three tectonic plates, whose gradual movements trigger earthquakes, Japan is one of the world's most quake-prone areas.
About 500 people were injured and a similar number of homes damaged or destroyed in an earthquake in July in Miyagi, 300km north of Tokyo.
Far worse was the quake that hit the city of Kobe eight years ago, killing more than 6000 people.
But the worst in Japan's history has been the Great Kanto earthquake in 1923, that measured 7.9 on the Richter scale and killed more than 140,000 people in Tokyo and the neighbouring city of Yokohama.