The 67-kilometre deep quake hit the southern part of Honshu's Ibaraki prefecture, north east of the capital Tokyo, at 01:10 am (1610 GMT Friday), the United States Geological Survey reported.
Its epicentre was 35 kilometres from Tokyo and there were no immediate reports of damage.
The quake, which struck just four kilometres from the city of Abiko, was also recorded by Japan's national weather agency.
Japan lies on the so-called "Ring of Fire", a series of seismic fault lines encircling the Pacific Ocean which create frequent seismic and volcanic activity.
Cooling systems at the Fukushima nuclear power plant were knocked out, sending reactors into meltdown and forcing tens of thousands of people to flee.
Last month, a deep 5.7-magnitude quake struck off the Honshu coastline while a 5.5-magnitude earthquake earlier in November rocked buildings in Tokyo. That tremor struck at a much shallower depth of 59 kilometres.
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