More than 850 people have reportedly been injured in the quake with at least 400 being treated at local hospitals, Russia Today reorted.
The quake hit at 9:26 p.m. local time (12:26 GMT) on Thursday, 11 kilometers (7 miles) east of the city of Kumamoto. It had a depth of 10 kilometers (6.2 miles).
An aftershock measuring 5.7 struck the region about 40 minutes after the quake, according to the Japan Meteorological Agency. The US Geological Survey (USGS) reported that a separate tremor measuring 5.9 struck a couple hours later.
Mashiko, a village close to the epicenter, suffered the worst damage, with over 20 buildings destroyed and several fires reported. The rescue operations are currently underway, with some 400 defense forces personnel deployed to help look through the debris during the night.
Local police said they received reports that several people were trapped under collapsed houses. They also said that several traffic lights lost power after the quake.
Some 16,500 households were left without electricity and 38,000 homes had no gas supplies.
Meanwhile, Japan's Nuclear Regulation Authority said there were no irregularities at three nuclear plants on the southernmost island of Kyushu and nearby Shikoku.
The USGS put the quake at a 6.0 magnitude.
The Japan Meteorological Agency originally issued a tsunami warning, but later canceled it.