A quake with a preliminary magnitude of 6.9 struck the Kyushu region at 9.19pm on Monday, the Japan Meteorological Agency said.
After an investigation, the JMA said the quake did not warrant special measures related to seismic activity in the Nankai Trough.
The Nankai Trough, where the Philippine Sea Plate is slipping under the Eurasia Plate at the bottom of the sea off the southwest coast of Japan, produces massive earthquakes about every 100-150 years.
Strong quakes nearby are seen as a potential indication that a megaquake could be more likely.
The JMA in August issued a week-long advisory for a "relatively higher chance" of a megaquake as powerful as magnitude 9 after a magnitude-7.1 quake hit the country's southwest.
After Monday's quake, tsunami advisories for waves of a maximum height of one metre were issued for the southern prefectures of Miyazaki and Kochi.
A 20cm tsunami was later recorded reaching Miyazaki city, public broadcaster NHK reported.
All tsunami advisories were later lifted.
There were no abnormalities reported at the Ikata Nuclear Power Plant in western Japan or the Sendai Nuclear Power Plant in Kagoshima prefecture, NHK said, referring to the two plants nearest to where the quake occurred.
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