The 6.3 tremor struck 16km (9.9miles) north-northwest of Nishinoomote on the island of Tangegashima in Kagoshima Prefecture.
United States Geological Survey (USGS) said the large earthquake hit at 12.39pm GMT (9.39pm local time).
The epicentre was located 117km (73 miles) away from the city of Kagoshima on Japan’s Kyushu Island, hitting at a depth of 35km.
There are no immediate reports of casualties or injuries.
No tsunami warnings are currently in place.
Where is Nishinoomote?
Nishinoomote sits at the northern side of Tanegashima, bordered by the East China Sea on the west and Pacific Ocean on the right.
The transport hub offers frequent ferry services between Japan’s island.
Tanegashima is the second largest of the Osumi Islands and is volcanic despite being fairly flat.
Today’s quake follows a 5.0 magnitude earthquake three days earlier in Kumamoto Prefecture on Kyushu island.
Japan’s Meteorological Agency said the January 3 tremor struck at a depth of 10km.
There were no reported casualties.
How often do earthquakes in Japan happen?
Earthquakes are common in Japan, one of the world’s most seismically active areas.
The region sits on the notorious Ring of Fire, home to 90 percent of the world’s earthquakes.
Japan accounts for about 20 percent of the world’s earthquakes of magnitude 6 or greater.