Thousands of dazed residents reportedly fled their homes and television footage showed damaged buildings, buckled roads and lumps of broken concrete in the streets after the quake on 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 650 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 Mashiki, scores of people gathered in front the town hall following the powerful shaking, some in tears and looking distressed, 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.
Some 350 military personnel were dispatched for rescue work on the island, spokesman Yoshihide Suga said, urging calm after the powerful shaking.
"I ask people in the disaster zone to act calmly and help each other," he said.
Several major manufacturers, including Honda, Bridgestone, Mitsubishi and Sony suspended operations at their factories in the area, according to reports.
The initial quake at 9:26 pm 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.
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.