The quake's epicentre was near the city of Kumamoto and measured at a depth of 40 km (25 miles), the US Geological Survey said.
A strong 7.0 earthquake hit southern Japan early Saturday, the US Geological Survey said, a day after another powerful tremor killed at least nine people in the same area.
The quake hit Kumamoto prefecture of the Kyushu main island at 1:25 am (1625 GMT Friday), the USGS said.
The Japan Meteorological Agency initially issued a tsunami warning for the western coast of the Kyushu island, where hundreds were injured in Thursday's quake, but later lifted it.
Public broadcaster NHK reported that waves of about one metre (3.3 feet) may have already reached shore.
After the 7.0 earthquake Saturday, the Japanese Meteorological Agency also reported several aftershocks hitting the area.
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