A total of 25 people have died in both earthquakes, according to current estimates.
The death toll in the latest Kyushu earthquake is 16 people, according to Kumamoto Prefecture's disaster management office. A previous earthquake that struck the area on Thursday had killed nine people.
The earthquake toppled buildings and shredded structures into pile of debris. At least 23 people were buried inside buildings, Chief Cabinet Secretary Yoshihide Suga said .
TV Asahi showed crews crawling over a collapsed roof in an attempt to find an elderly couple. An 80-year-old man was pulled from the rubble, TV Asahi said.
The tremors appear to have caused extensive damage, overturning cars, splitting roads and triggering a landslide as shown by TV Asahi footage. The area was rocked by as many as 165 aftershocks, some of them as strong as magnitude-5.3 struck in the hours after the quake.
Television images showed mostly desolate streets, shards of broken glass on the streets and people huddled outside.
Japan's Fire and Disaster Management Agency said 7,262 people have sought shelter at 375 centers since Friday in Kumamoto Prefecture. Suga said 20,000 self-defense forces are being deployed to the region for rescue efforts.
Japan's "Ring of Fire"
The U.S. Geological Survey
reported that the latest quake struck just west-southwest of Kumamoto-shi and about 8 miles south-southeast of Ueki, the epicenter of the late Thursday tremor that left nine dead.
"No question, this is a large and very important earthquake," said Doug Given, a geophysicist with the USGS. "And it will do a lot of damage."
Given noted: "The four islands of Japan are on the edge of what's traditionally been known as the 'Ring of Fire'" -- a stretch along parts of the Pacific Ocean prone to volcanoes and earthquakes.
Victor Sardina, a geophysicist in Honolulu, Hawaii, told CNN that the latest quake was about 30 times more powerful than Thursday's deadly tremor. He predicted "severe, serious implications in terms of damage and human losses."
The shallow depth of the quake -- about 10 kilometers, or 6 miles -- and the densely populated area where it struck could prove to be devastating, according to experts.
The quake prompted the Japan Meteorological Agency to issue a tsunami advisory
for coastal regions of Japan on the Ariake Sea and Yatsushiro Sea around 2 a.m. Saturday (1 p.m. ET Friday). The agency subsequently lifted all tsunami warnings and advisories.
Japanese media reported a small scale eruption of Mt. Aso around 8:30 a.m. local time Saturday. It was unclear whether the eruption occurred in relation to the earthquake, according to the Japan's meteorological agency.
'Buildings were swaying and cracking'
"This looks like it's going to be a very damaging earthquake. I think we can expect that this is going to be far worse" than Thursday's tremor, said Tom Jordan, director of the Southern California Earthquake Center.
In short video posted to Instagram, people standing in the parking lot of a 7-Eleven in Kumamoto let out screams following an aftershock.
Journalist Mike Firn in Tokyo told CNN he felt the trembles in a building some 900 kilometers, or more than 550 miles away from the epicenter.
"The building started shaking," he said. "It was swaying quite strongly for over a minute. ... Buildings were swaying and cracking."
The latest tremor suggests that the earthquake on Thursday was a foreshock, though USGS expert cautioned "that's not to say that the Earth can't produce a bigger earthquake still to follow."
"But statistically, it's more likely that this latest event will be followed by aftershocks, which are all smaller."
Prime Minister on the way to the site
Prime Minister Shinzo Abe will visit the earthquake-hit area in Kumamoto prefecture later Saturday, he said at a meeting at emergency response headquarters in Tokyo.
"I would like to see the site with my own eyes and hear from the victims directly," Abe said.
Search crews were continuing to dig through rubble looking for other people trapped under collapsed buildings.
The Thursday quake struck near Ueki, the U.S. Geological Survey said. Dozens of smaller aftershocks followed.
"The ground shook for about 20 seconds before the 6.2-magnitude quake stopped," witness Lim Ting Jie had said.
Two deaths occurred in Mashiki, the Kumamoto prefecture office said. One person died in a collapsed house, and the other died in a fire caused by the quake. Journalist Mike Fern told CNN that scores of buildings had either collapsed or caught fire, while the tremors triggered landslides, tore up roads and in one case, derailed a bullet train.
Nearly 800 people were injured, 50 severely. The prefecture office said 44,449 people had been evacuated.
Baby pulled from rubble after earlier quake
Japan had already been coping with a previous earthquake on Kyushu island on Thursday. During the search and recovery effort for the first earthquake, rescuers found an 8-month-old baby girl alive in the ruins of a home destroyed by the earlier quake on Japan's Kyushu island.
Rescuers had been told there was a baby inside the collapsed house, but aftershocks from the quake prevented the use of heavy equipment at the site. After six hours after the infant was trapped, she was pulled from the rubble early Friday.
"It was miracle she was unharmed," said Hidenori Watanabe, a spokesman for the Kumamoto Higashi fire department.
Fifty rescuers -- wearing dark uniforms and white hard-hats with lights -- scoured the large pile of rubble that just hours before had been a home. The infant's mother and grandmother had managed to escape.
The little girl was finally found safe amid the debris in a space under one of the house's pillars, according to Watanabe.
This happened in the middle of the night, in an area lit only by spotlights.
Carefully, rescuers passed the barefooted baby to one another, before she finally got to crews on the ground and was taken swiftly away.
A high-risk area
The largest recorded quake to hit Japan came on March 11, 2011, when a magnitude-9.0 quake centered 231 miles (372 kilometers) northeast of Tokyo devastated the country.
That quake triggered a massive tsunami that swallowed entire communities in eastern Japan. It caused catastrophic meltdowns at the Fukushima Daiichi nuclear power plant.
The disaster killed about 22,000 people -- almost 20,000 from the initial quake and tsunami, and the rest from health conditions related to the disaster.