In the Philippines, the Philippine Institute of Volcanology and Seismology (Phivolcs) said the tsunami would not affect any part of the country but said it could affect localities near the epicenter.
The Japan Meteorological Agency said epicenter of the magnitude 6.8 quake that struck at 9:43 a.m. on Monday was at a shallow point near the Yonaguni islands.
The tsunami warning remained in force for over an hour after the quake struck, but authorities said it was unclear if a tsunami had hit shores of islands in the area.
Television footage of a nearby island showed calm seas, but residents were warned to stay away from the shore.
The public broadcaster NHK said there were no initial reports of damage.