Workers in Japan suspended the Hamaoka powerstation's number-five reactor at 1:00 pm (0400 GMT) in a bid to avoid a repeat of the atomic emergency sparked by the March 11 earthquake and tsunami.
"The shutdown was confirmed after we inserted all 205 control rods into the reactor," said Hiroaki Oobayashi, a spokesman for the plant's operator Chubu Electric Power Co.
Seismologists have long warned that a major earthquake is overdue in the Tokai region southwest of Tokyo where the Hamaoka plant is located.
Naoto Kan, Japanese prime minister called for Hamaoka's closure last week, eight weeks after the 9.0-magnitude quake and tsunami which knocked out the cooling systems at the Fukushima Daiichi plant, sparking the world's worst atomic crisis in 25 years.
Kan has insisted the Hamaoka plant should stay shut while a higher sea wall is built and other measures are taken to guard it against natural disasters. The process is expected to last a few years.
The complex, located on the Pacific coast some 200 kilometres (125 miles) northeast of Tokyo, has five reactors but only two have been running recently -- numbers four and five. Reactor number four was suspended on Friday.
Reactors one and two, built in the 1970s, were stopped in 2009, and three is undergoing maintenance.
Hamaoka accounts for almost 12 percent of the output of Chubu Electric, which serves a large part of Japan's industrial heartland, including many Toyota car factories.
Kan told the governor of Fukushima prefecture in a meeting Saturday that he was considering legislation to compensate people forced to flee their homes in the wake of the nuclear crisis.
More than 80,000 people have been forced from homes, farms and businesses in a 20-kilometre (12-mile) zone around the plant which has leaked radiation into the air, ground and sea.
The governor, Yuhei Sato, said Kan told him: "The government will firmly put a special law in place and take the responsibility for compensation."
Sato told reporters that the existing law on nuclear accidents was limited in scope as it does not cover damage such as the cost of misinformation on radioactive contamination of farm, fishery and other products from Fukushima.
"Harmful rumours have caused unimaginable damage," he said.
On Friday, Kan's centre-left government launched a rescue plan to help the Fukushima plant's owner, Tokyo Electric Power Co., foot the bill for the disaster.
TEPCO faces compensation payments worth tens of billions of dollars for victims of the accident.
TEPCO and the government have yet to release estimates for the payout bill, but analysts say it could range from four trillion yen ($50 billion) to 10 trillion yen depending on how long the nuclear crisis lasts.
To help TEPCO, Asia's biggest electric power company, meet its obligations, Kan's government decided on a financial aid plan paid for mostly with new government bonds.
The scheme will give the government a stronger hand in supervising TEPCO, save the biggest of Japan's 10 utilities from bankruptcy and prevent turmoil on financial markets in the world's third-largest economy.