No damage or injuries were immediately reported, and Japan's meteorological agency said there was no danger of a tsunami.
The temblor hit at 12:25 p.m. local time (0325 GMT), with the epicenter near the Ogasawara Islands, about 500 miles (800 kilometers) south of the main Japanese island, the agency said. It struck at a depth of 300 miles (480 kilometers).
Japan's meteorological agency reported a magnitude of 6.9, however, the U.S. Geological Survey said the quake was 6.6. The reason for the discrepancy was not immediately clear.
The Ogasawara are known as the Bonin Islands outside of Japan.
Japan is one of the most earthquake-prone countries in the world. In 1995, a quake of magnitude 7.2 killed 6,400 people in the western port city of Kobe.