The Japan Meteorological Agency said the quake registered a magnitude of 6.9 but was centred offshore near Torishima, about 370 miles south of Tokyo.
A quake of that magnitude is at the upper range of a "strong" earthquake, capable of causing major damage to buildings.
The crippled Fukushima nuclear plant was not affected.
Most buildings in Japan meet modern standards for earthquake resistance and would withstand shaking that might cause major damage elsewhere.
Despite the remoteness of the epicentre, tremors were felt from the north of the main island of Honshu to the west.
No injuries or damage was reported.