A tsunami warning was issued by the Japan Meteorological Agency that was lifted some 30 minutes after the quake hit the islands.
The quake's epicentre was located at 10 km below sea level off the nearby Ishigaki island, according to the agency.
Meanwhile, an emergency task force has been set up to coordinate the government's response to the earthquakes at the prime minister's office.
Japan is one of the most earthquake-prone countries in the world, and it was hit by a series of tremors last week.
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