The quake hit off the northeastern coast of Amami Oshima island in southern Japan at a depth of 37 miles (60 kilometers).
The small island is about 800 miles (1,300 kilometers) southwest of Tokyo.
The offshore quake also shook Kagoshima and dozens of towns on the southern main island of Kyushu, but the temblor was not felt in Tokyo or elsewhere in the country, the agency said.
Japan is one of the world's most earthquake-prone countries. In 1995, a magnitude-7.2 quake in the western port city of Kobe killed 6,400 people.
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