The magnitude 6.0 quake hit at a depth of 10 kilometres (6.2 miles) in waters off the island of Miyako in the southern Okinawan chain, according to the US Geological Survey.
Japan's Meteorological Agency warned of small changes in sea levels but no tsunami.
Miyako, with a population of about 55,000, sits some 1,840 kilometres (1,143 miles) southwest of Tokyo and about 380 kilometres east of Taipei.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year, though damage is often slight thanks to rigorous building codes and broad earthquake awareness.
More than 18,500 people were left dead or missing and three reactors went into meltdown at the Fukushima nuclear plant.
It was Japan's worst disaster in the post World War II-era.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)