The quake struck at 7:20 a.m. Saturday (2220 GMT Friday) just off the coast of Hokkaido, the northernmost of Japan's four main islands, the agency said.
The temblor rattled areas along Hokkaido's southern coastline as well as the northern reaches of Japan's main island of Honshu, but there were no immediate reports of damages or injuries.
Japan is one of the world's most earthquake-prone countries because it sits atop four tectonic plates.
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