A rapid fluctuation in sea levels flooded some parts of Nagasaki City on Thursday night.
Port authorities called on residents to stay alert ahead of high tide expected at around 9 a.m. on Friday.
Rapid fluctuations in sea levels in cycles of several to several dozen minutes can be triggered by changes in atmospheric pressure and some other factors.
The local weather observatory says the phenomenon was observed at Nagasaki port just after 8 p.m. on Thursday. As it coincided with high tide, the sea level surged by up to one meter, flooding some parts of the city.
Local police say the water was up to 30 centimeters deep at some locations but no one was hurt.
Weather officials warn that a recurrence could damage vessels anchored at the port and flood the city's low-lying areas.