The quake struck at 7:37 am (2237 GMT Saturday), in Ibaraki prefecture, north of the capital, at a depth of 59 kilometres (37 miles), the US Geological Survey said.
The crippled Fukushima nuclear power plant was shaken by the quake but there were no abnormalities reported, the plant's operator said.
The quake lasted about 30 seconds and was felt by many people in Tokyo.
High-speed Shinkansen trains were stopped briefly for a track check, but quickly returned to normal operation.
More than 18,000 people died when a 9.0-magnitude sub-sea earthquake sent a towering tsunami barrelling into Japan's northeast coast in March 2011 in the country's worst post-World War II disaster.
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