The quake hit at 4:42 pm (0742 GMT) off Kyushu at a depth of 25 kilometres (16 miles), the United States Geological Survey said.
The USGS had initially reported two strong quakes, with magnitudes of 6.9 and 7.1, but later said there had only been one tremor.
The Japan Meteorological Agency (JMA) also said there was one quake with a magnitude of 7.1.
Broadcaster NHK showed footage of traffic lights shaking violently in Miyazaki on Kyushu's southeast coast.
"The surface of the sea is wavering. I felt an intense jolt when the quake happened which lasted for between 30 seconds and a minute," one local official told NHK.
The broadcaster also reported that three people were hurt in Miyazaki but gave no indication of the extent of their injuries.
Tsunamis of up to one metre were initially expected to arrive or had arrived in some coastal areas in Kyushu and Shikoku islands, the JMA said.
The agency also said a small tsunami was possible in Chiba, about 850 kilometres (530 miles) from the epicentre.
"Tsunamis will strike repeatedly. Please do not enter the sea or approach the coast until the warning is lifted," the JMA said on social media platform X.
However, tsunamis of only 50 cm, 20 cm, and 10 cm were confirmed to have hit some places, including the port of Miyazaki, more than an hour after the quake, it said.
The Pacific Tsunami Warning Center issued a warning that said hazardous tsunami waves were possible within 300 kilometres (185 miles) of the epicentre.
No abnormalities were reported at atomic power plants in the area, according to the nuclear regulation authority.
Government spokesman Yoshimasa Hayashi said "damage to people and property" was still being assessed.
"In view of this situation, the prime minister instructed (officials) to provide the public with timely and accurate information on tsunamis and evacuations," he said.
Unverified footage shared on social media showed only minor damage, including dishes and books that had fallen off shelves and a small wall that had collapsed in a car park.
- Task force -
The Japanese government set up a special task force in response to the quakes, according to a statement.
Sitting on top of four major tectonic plates along the western edge of the Pacific "Ring of Fire", Japan is one of the world's most tectonically active countries.
The archipelago, home to around 125 million people, experiences around 1,500 jolts every year and accounts for around 18 percent of the world's earthquakes.
The vast majority are mild, although the damage they cause varies according to their location and the depth below the Earth's surface at which they strike.
Still, even large quakes usually cause little damage thanks to special construction techniques and strict building regulations in the world's number four economy.
At least 318 people were killed when an earthquake hit the Noto peninsula on the Sea of Japan side of the main island of Honshu on New Year's Day.
The January 1 quake and its aftershocks toppled buildings, caused fires and knocked out infrastructure.
Japan also routinely holds emergency drills to prepare for a major quake.
It is haunted by the memory of a colossal 9.0-magnitude undersea quake off northeastern Japan in March 2011, which triggered a tsunami that left around 18,500 people dead or missing.
It sent three reactors into meltdown at the Fukushima nuclear plant, causing Japan's worst post-war disaster and the most serious nuclear accident since Chernobyl.
In March 2022, a 7.4-magnitude quake off the coast of Fukushima shook large areas of eastern Japan, killing three people.
The capital Tokyo was devastated by a huge earthquake a century ago in 1923.
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