An alarm sounded "during reactor-start-up procedures" at Kashiwazaki-Kariwa north-west of Tokyo but the reactor remained "stable", Tokyo Electric Power Company (Tepco) spokesperson Takashi Kobayashi said.
Reactor number six restarted on Wednesday a day later than planned due to an alarm malfunction - the first at the plant to be turned on since the 2011 Fukushima disaster.
Japan shut down all of its 54 reactors after a 9.0 magnitude earthquake triggered a meltdown at its Fukushima plant 15 yearsa go, causing one of the worst nuclear disasters in history.