The earthquake, which hit at around 0153 GMT, was recorded at magnitude 7.0 according to a technique similar to the Richter scale, but adjusted for Japan's geological characteristics.
At the moment there are no reports of casualties or fires and the tsunami warnings were lifted about an hour after the quake struck.
However, authorities are advising people to stay away from the coast.
There are also reports of broken water mains and high speed bullet trains and other trains and subways suspending operations.
Fukuoka Airport suspended operations for checks but there was no damage to the airport, which later reopened, a private TV broadcaster said.
Some power outages are reported, but the Kyushu Electric Power Co. said neither of its two nuclear power plants in Saga and Kagoshima prefectures was affected by the earthquake.
The quake was felt as far away as Seoul, the capital of South Korea.
Japanese TV showed footage of cracks in pavements and walls of buildings leaning to one side in Kyushu.
"It was so strong that I thought my house would collapse. I rushed to turn off the stove and evacuated. I felt uneasy because it was my first experience"
The focus of the quake was off the western coast of Fukuoka Prefecture, about 900km southwest of Tokyo on the island of Kyushu, and the depth was shallow, the meteorological agency said.
"It was so strong that I thought my house would collapse. I rushed to turn off the stove and evacuated. I felt uneasy because it was my first experience," Toshiyuki Yasukawa, an official in the town of Sue in Fukuoka, said.
An official at Nakama city hall in Fukuoka said: "There was a report of a water leak at a home and that a water pipe burst in an apartment complex. But there are no reports of any injuries."
Officials gathered at the prime minister's official residence in Tokyo to monitor the situation.
"I've received reports about the earthquake. Since there have been tsunami warnings, I have issued instructions to watch the situation closely"
Japanese prime minister
"I've received reports about the earthquake. Since there have been tsunami warnings, I have issued instructions to watch the situation closely," Prime Minister Junichiro Koizumi was quoted as telling reporters.
Earthquakes are common in Japan, one of the world's most seismically active areas. The country accounts for about 20% of the world's earthquakes of magnitude 6 or greater.
In October 2004, an earthquake with a magnitude of 6.8 struck the Niigata region in northern Japan, killing more than 40 people and injuring more than 3000.
That was the deadliest quake since a magnitude 7.3 tremor hit the city of Kobe in 1995, killing more than 6400.