The agency said the advisory covered the nearby Ariake and Yatsushiro Seas on the western coasts of Kumamoto, Nagasaki, Fukuoka and Saga prefectures about 560 miles south west of Tokyo.
The advisories were lifted within two hours.
The US Geological Survey initially said the earthquake had a magnitude of 7.1, but revised it later to 6.8.
Japan’s prime minister Sanae Takaichi, in a message posted on X, urged residents to avoid the coastline where a tsunami of up to one metre was predicted.
She said her government has set up a task force to gather information, assess possible damage and prepare for rescue operations if needed.
Ms Takaichi later told reporters that there have been reports of a number of injuries and damages to roads, bridges and buildings, as well as blackouts and fire, though details are still unclear.
Ms Takaichi warned people cooking to be careful with fire and with shards of broken glass.
“We are putting people’s lives as the top priority,” Ms Takaichi said, urging residents in the strongly shaken areas to use caution in light of possible strong aftershocks.
Kyodo News agency said a hospital in Yatsushiro city accepted about 40 people with injuries from the quake.
A train was derailed and fell on its side at the Yatsushiro station, and stone walls were damaged at the Kumamoto castle, Kyodo said.
Yozo Kai, a priest at a Shinto shrine in the nearby town of Mashiki, said a few stone lanterns fell down.
“I worried if the main hall and the gate would tilt again,” he told Kyodo.
“The shaking reminded me of the Kumamoto quake (10 years ago) and I was frightened,” said Hiroki Shimoda, an official at the Mifune town hall, who saw rooftiles of nearby homes crash down to the ground.
Shinji Kiyomoto, JMA’s earthquake and tsunami countermeasures planning officer, told a news conference that the shallow earthquake was triggering active seismic activity in the area, urging residents to especially be cautious over the next two to three days for another big quake.
He said, however, that no tsunami was observed from the inland quake.
Japan’s Fire and Disaster Management Agency said there were no reports of damage to major public facilities and infrastructure in the region, though authorities were still assessing the extent of damage from the quake.
Local fire departments received many emergency calls.
Japan’s Nuclear Regulation Authority said no abnormalities were found at three nearby nuclear power plants.
Shinkansen bullet trains and local trains in Kyushu have been suspended for safety checks, while the runway at the Aso Kumamoto Airport was closed, with “no prospect of resuming operations”, according to a notice on the airport’s website.
The Japanese Defence Ministry said it dispatched aircraft to the area to assess the situation.
Kumamoto was hit with a deadly quake in 2016 that left more than 50 people dead, 1,800 injured and tens of thousands of homes damaged or destroyed.