The reactor at the Takahama power plant in central Fukui region halted at around 3:20 pm (0620 GMT) after an alarm warning of a rapid decrease in the number of neutrons, according to the Nuclear Regulatory Authority (NRA).
But the NRA said in a statement that the "reactor is cooling normally" and "there is no impact on the surrounding environment", as no abnormalities in radioactive levels were detected.
Operator Kansai Electric Power Co said in a statement it was still investigating the cause.
Fukui regional officials also said it was unclear what had caused the alarm to go off, according to public broadcaster NHK, though they noted there were no abnormalities in reactor temperature or pressure.
The reactor, one of four at the Takahama plant, only restarted operations late last year after routine inspections.
There are 33 reactors in Japan, but fewer than a third are back in action more than a decade after a deadly tsunami in March 2011 caused a meltdown at the Fukushima nuclear plant.
Not all are operational year-round, and the country is heavily dependent on imported fossil fuels.
With Japan facing its most severe energy crisis in decades, Prime Minister Fumio Kishida said in August that the country should consider building next-generation nuclear reactors.
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