The Japan Meteorological Agency said the quake registered magnitude 7.1 and was centered in waters off the eastern coast of Japan's southern main island of Kyushu at a depth of about 30 kilometers (18.6 miles), CNBC reported.
The quake most strongly shook Nichinan city and nearby areas in Miyazaki prefecture on Kyushu island.
The agency said tsunami waves of up 50 centimeters (1.6 feet) were detected along parts of Kyushu's southern coast and the nearby island of Shikoku about a half hour after the quake struck.
Seismologists were holding an emergency meeting to analyze whether the quake had affected the nearby Nankai Trough, the source of past devastating earthquakes.
Chief Cabinet Secretary Yoshimasa Hayashi said officials were assessing possible injuries or serious damage, though none were immediately reported. He urged residents of the affected region to stay away from the coastline.
Japan's NHK public television said there were reports of broken windows at the Miyazaki airport near the epicenter.
The Nuclear Regulation Authority said all 12 nuclear reactors, including three which are currently operating, on Kyushu and Shikoku remained safe.
Earthquakes in areas with nuclear power plants have been a major concern since a massive earthquake and tsunami in March 2011 triggered the Fukushima nuclear disaster.
Japan sits on the Pacific "Ring of Fire," the line of seismic faults encircling the Pacific Ocean, and is one of the world's most earthquake-prone countries.
An earthquake on Jan. 1 in Japan's north-central region of Noto left more than 240 people dead.