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The tremor hit off southwestern Tanegashima island 1,000 kilometres (620 miles) southwest of Tokyo at 9:58 pm (1258 GMT).
The US Geological Survey measured the tremor at 6.1 magnitude with a depth of 21 kilometres while the Japan Meteorological Agency put it at 5.7 and a shallower 10 kilometres.
A massive magnitude 9.0 earthquake and following tsunami devastated northeast Japan on March 11, with nearly 28,000 people dead or missing.
A number of strong aftershocks have shaken the country. A magnitude 7.1 tremor hit the region late Thursday.