Seiboku Sueyoshi, an official in Naha city, southern Okinawa, said: "First there was a strong vertical shake, then sideways. The strong quake lasted for about 10 seconds."
Small waves of around 10cms were recorded in southern areas of Okinawa island, Japan’s Meteorological Agency said, adding that additional minor surges of the sea level may still be seen near the island.
'Big one' feared
Earthquakes are common in Japan, one of the world's most seismically active areas.
The country accounts for about 20 per cent of the world's earthquakes of magnitude 6 or greater.
Geologists warn that Japan is overdue for a massive and potentially devastating earthquake.
They point to an 87 per cent chance that the "Big One" - a magnitude-eight earthquake or worse - will strike the greater Tokyo region, home to around 35 million people, within the next 30 years.
The last time a massive earthquake struck Tokyo was in 1923, when the Great Kanto Earthquake claimed more than 140,000 lives, many of them in fires.
In October 2004, an earthquake with a magnitude of 6.8 struck the Niigata region in northern Japan, killing 65 people and injuring more than 3,000.
That was the deadliest quake since a magnitude 7.3 tremor hit the city of Kobe in 1995, killing more than 6,400.