The quake, which shook buildings in Tokyo, struck at 11:19 am (0219 GMT), 83 kilometres (52 miles) north of the capital and at a depth of 20 kilometres, the USGS said.
Operator Tokyo Electric Power Co. (TEPCO) said the tremor did not disrupt the emergency crews who are working around the clock to cool crippled reactors at a nuclear plant hit by a devastating earthquake and tsunami last month.
That earthquake -- the biggest ever recorded in Japan -- struck on March 11, triggering a huge tsunami and leaving 13,591 people dead, with another 14,497 still unaccounted for.
Tens of thousands of people lost their homes, while many others were forced to evacuate after a series of explosions at the Fukushima Daiichi nuclear plant sent radiation spewing into the air.
The radiation leaks have resulted in bans on produce from the affected area and hurt the fishing and farming industries because of public fears over radioactivity in food.
On Friday, Japan's government ordered TEPCO to offer payouts to tens of thousands of people made homeless by the ongoing crisis.
The total cost from collapsed or damaged houses, factories and infrastructure such as roads and bridges is estimated to reach 16-25 trillion yen over the next three fiscal years, according to the Cabinet Office.
There were no immediate reports of any damage or casualties from Saturday's quake, which the Japan Meteorological Agency said had a magnitude of 5.9 and struck at a depth of 70 kilometres underground.
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