Tens of thousands of people reportedly fled their homes and television footage showed damaged buildings, buckled roads and lumps of broken concrete in the streets after the 6.5-magnitude quake struck the southwestern island of Kyushu.
NHK footage showed what appeared to be a house ablaze and firefighters dousing it with water, one of several fires reportedly sparked by the quake that left at least 780 injured, according to the public broadcaster.
"I felt quite strong jolts, which I had never experienced before," Shunsuke Sakuragi, a prefectural official in the city of Kumamoto, told AFP.
"People were shocked but I have not seen any extreme confusion in the city."
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In the neighbouring town of Mashiki, scores of people gathered in front the town hall following the powerful shaking, some in tears while others wrapped themselves in blankets to ward off the nighttime chill.
"We also received information indicating a few people were under collapsed houses," said Sakuragi.
As the death toll rose in the night -- earlier reports said two people had died -- an eight-month-old baby girl was pulled from the rubble alive and unharmed, NHK reported.
Some 350 military personnel were dispatched for rescue work on the island, spokesman Yoshihide Suga said, appealing for calm.
"I ask people in the disaster zone to act calmly and help each other," he said.
Officials in Kumamoto prefecture said they were considering evacuating a hospital that was badly damaged, while several major manufacturers including Honda, Bridgestone, Mitsubishi and Sony suspended operations at their factories in the area, according to reports.