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The tremor occurred at 10:18 a.m. local time (0118 GMT) and was centred in Shimane Prefecture, the agency said. Authorities reported no major damage following the quake.
The US Geological Survey recorded the earthquake at a slightly lower magnitude of 5.8, reflecting common variations between monitoring agencies.
In the western city of Yasugi, the quake registered upper five on Japan’s Shindo scale, a level at which heavy furniture can topple and drivers may experience difficulty controlling vehicles.
Officials said the same area was later rattled by smaller aftershocks, measuring 4.5, 5.1, 3.8, and 5.4, all without triggering tsunami alerts.
Japan lies along the western edge of the Pacific Ring of Fire, where several tectonic plates meet, making it one of the most earthquake-prone countries in the world. The nation, home to about 125 million people, experiences roughly 1,500 earthquakes each year. While most are minor, the level of damage depends on factors such as location and depth.