The restart, initially scheduled for Tuesday, had been pushed back after another technical issue related to the control rods' removal was detected last weekend.
The restart of the world's largest nuclear power plant was suspended in Japan on Thursday just hours after the process began, its operator said, but the reactor remains "stable."
Operations to relaunch a reactor at the Kashiwazaki-Kariwa plant in Niigata province, closed since the 2011 Fukushima disaster, began late on Wednesday after it received the final green light from the nuclear regulator despite divided public opinion.
But its operator the Tokyo Electric Power Company (TEPCO) said that "an alarm from the monitoring system...sounded during the reactor startup procedures," causing them to suspend operations.
"We were investigating the malfunctioning electrical equipment," spokesperson Takashi Kobayashi said and "once it became clear that it would take time, we decided to reinsert the control rods in a planned manner."
The reactor "is stable and there is no radioactive impact outside," he said.
Control rods are a device used to control the nuclear chain reaction in the reactor core, which can be accelerated by slightly withdrawing them, or slowed down or stopped completely by inserting them deeper.
The restart, initially scheduled for Tuesday, had been pushed back after another technical issue related to the rods' removal was detected last weekend, a problem that was resolved on Sunday, according to TEPCO.
Kashiwazaki-Kariwa is the world's biggest nuclear power plant by potential capacity, although just one reactor of seven was restarted.
The facility was taken offline when Japan pulled the plug on nuclear power after a colossal earthquake and tsunami sent three reactors at the Fukushima atomic plant into meltdown in 2011.
However, Japan now wants to revive atomic energy to reduce its reliance on fossil fuels, achieve carbon neutrality by 2050 and meet growing energy needs from artificial intelligence.
Kashiwazaki-Kariwa is the first TEPCO-run unit to restart since 2011. The company also operates the stricken Fukushima Daiichi plant, now being decommissioned.
Public opinion in Niigata is deeply divided. Around 60% of residents oppose the restart, while 37% support it, according to a survey conducted in September.
"It's Tokyo's electricity that is produced in Kashiwazaki, so why should the people here be put at risk? That makes no sense," Yumiko Abe, a 73-year-old resident, told the AFP news agency during a protest earlier this week.
Earlier this month, seven groups opposing the restart submitted a petition signed by nearly 40,000 people to TEPCO and Japan's Nuclear Regulation Authority, saying that the plant sits on an active seismic fault zone and noted it was struck by a strong quake in 2007.