The initial magnitude 6 tremor struck 11km east of the city of Kumamoto on Thursday, according to the US Geological Survey (USGS).
It said the magnitude was 6.2 but later revised it down.
There was no tsunami warning, but at least one person was killed after being crushed by a collapsing building, local media reported.
More than 400 people were taken to hospital.
The Kyodo news agency said some 44,400 people had also been evacuated and more than 100 aftershocks had been recorded since the quake, which struck shortly before 9.30pm local time.
Footage from public broadcaster NHK showed firefighters tackling a blaze in a building in Mashiki, a town of about 34,000 people near the epicentre of the quake.
Source: AAP
"We will do our utmost and carry on with life-saving and rescue operations throughout the night," Prime Minister Shinzo Abe told reporters.
Japanese media showed residents, some of them wrapped in blankets, huddling in parking lots and other open space for fear of further building collapses.
"The apartment building I live in is now tilting. Everything fell down inside. It's a mess," a male resident in Mashiki said on NHK.
About 16,500 households in and around Mashiki were without electricity as of 2 am, according to Kyushu Electric Power Co Inc.
The Nuclear Regulation Authority said there were no irregularities at three nuclear plants on the southern major island of Kyushu and nearby Shikoku.
In March 2011, a quake of magnitude 9 struck offshore north of Tokyo, causing tsunami waves along the coast that killed nearly 20,000 people and triggered a nuclear power plant meltdown.
After Thursday's quake, some high-speed trains were halted as a precaution.
A house collapses following the earthquake in Mashiki, near Kumamoto city, southern Japan, early Friday, April 15, 2016. Source: AAP
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