Thursday's magnitude-6.2 quake caused shaking at some places as intense as the huge earthquake that hit the country in 2011, Japan's seismology office said.
That quake sparked a huge tsunami and nuclear meltdown at a power plant in Fukushima.
Most of those who died in Thursday's quake were in the town of Mashiki where an apartment building collapsed and many houses were damaged.
More than 1,000 people were injured.
Some 40,000 people had initially fled their homes, with many of those closest to the epicentre spending the night outside, as more than 130 aftershocks had hit the area.