17 February 2015, 06:42 GMT
The quake hit 130 km off Miyako at 4.31 GMT at a depth of 10 km.
The agency said the temblor might lead to some change in tidal levels but no material damage was expected.
Earlier this week, a 6.9 magnitude quake struck off Japan’s northeast coast, triggering a tsunami advisory and evacuation warnings in coastal towns.
