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.
A camera in one of its offices showed violent shaking as the earthquake hit, with computer monitors and files tumbling off shelves as employees fell to the floor to take cover.
"I felt quite strong jolts, which I had never experienced before," Shunsuke Sakuragi, a prefectural official in the city of Kumamoto, told AFP.
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"People were shocked but I have not seen any extreme confusion in the city."
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.
READ: Three dead in Japan earthquake
At least nine people were confirmed dead, a Kumamoto disaster management official said.
"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.
Nuclear reactors unaffected
The initial quake at 9:26 pm (1226 GMT) was followed two and a half hours later by another strong one measuring 6.4 magnitude in the same region, according to the Japan Meteorological Agency.
In total, more than 30 earthquakes rocked the region after the first hit, and Prime Minister Shinzo Abe convened a meeting of emergency management officials, according to Suga.
Japan's two sole operating nuclear reactors, located on Kyushu, were functioning normally, an official at the Sendai plant told AFP.
Japan, one of the most seismically active countries in the world, has been particularly on edge over the vulnerability of nuclear power plants after a massive undersea quake on March 11, 2011 that sent a tsunami barrelling into the country's northeast coast.
Some 18,500 people were left dead or missing, and several nuclear reactors went into meltdown at the Fukushima plant in the worst atomic accident in a generation.
Train services on Kyushu were temporarily halted after Thursday's earthquake and a super fast bullet train derailed, though it was not carrying passengers at the time, said Yusuke Nanri, a spokesman for operator JR Kyushu.
He said it was not clear if the train was travelling or stationary when the quake struck.
The first earthquake hit at a relatively shallow depth of 10 kilometres (6.2 miles), according to the meteorological agency, which said there was no danger of a tsunami. The US Geological Survey measured the earthquake as 6.2 magnitude.
Aftershocks were likely to continue for about a week, officials said.
Japan sits at the junction of four tectonic plates and experiences around 20 percent of the world's most powerful earthquakes.
But rigid building codes and strict enforcement mean even powerful tremors frequently do only limited damage.