The quake rocked wide areas of the main southern island of Kyushu at 12:36 am (1536 GMT Monday), the meteorological agency said. It was focused off Tanegashima island, 1,000 kilometers (620 miles) southwest of Tokyo.
"We have no reports of damage or injuries," a Kyushu police spokesman said.
The tremor did not cause tsunami waves.
An earthquake measuring 6.9 on the Richter scale shook northern Japan a week ago, forcing hundreds of residents to flee their homes as small tsunami waves hit the Pacific coast.
Japan endures 20 percent of the world's major earthquakes.