At least nine people died and more than 860 were injured, officials said, as shaking toppled buildings.
The magnitude 6.5 quake struck at 21:26 on Thursday (12:26 GMT), near Kumamoto city, on the island of Kyushu.
The intensity of the quake was similar to that of the one in 2011, which sparked a huge tsunami and nuclear meltdown in Fukushima.
Most of those who died in Thursday`s quake were in the town of Mashiki, near Kumamoto, where an apartment building collapsed and many houses were damaged.
More than 40,000 people had initially fled their homes, with many of those closest to the epicentre spending the night outside. Some are now returning to their homes despite the frequent aftershocks.
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