Prime Minister Naoto Kan said at a news conference Friday evening the shutdown was requested for safety reasons, citing experts' forecast of a 90 percent probability of a quake with magnitude of 8.0 or higher striking central Japan within 30 years.
"It was a decision made after thoroughly considering people's safety," Kan told a news conference.
The government asked operator Chubu Electric Power Co. to suspend two running reactors and a third already shut for a regular inspection at the Hamaoka nuclear plant in Shizuoka, 155 miles (250 kilometers) west of Tokyo.
"If an accident occurs at Hamaoka, it could create serious consequences," Kan said.
Chubu Electric did not immediately say if it would suspend operations at the Hamaoka plant, which is just 100 meters off the Pacific coast.
A safety review of all Japan's 54 nuclear plants was prompted by the radiation crisis at the Fukushima Dai-ichi nuclear plant, which was crippled by the March 11 earthquake and tsunami that also left more than 25,000 people dead and missing on the northeast coast.
The Hamaoka plant is the only one so far where the government has asked that operations be halted until the utility can implement safety measures. Officials estimate the shutdown could last two years.
Since the March 11 disasters, Chubu Electric has drawn up safety measures that include building a seawall nearly a mile (1.5 kilometers) long over the next two to three years.
"The height of the seawall is at least 12 meters. We have come up with this safety measure after the March quake and tsunami," said Takanobu Yamada, an official at Chubu Electric.
The company also planned to erect concrete walls along 18 water pumps at the plant. Yamada said the walls aimed to protect the pumps from damage from an earthquake and tsunami, and it will take a year or one and a half years to complete the construction.
The plant does not have a concrete sea barrier now, but sandhills between the ocean and the plant are about 32 to 50 feet (10 to 15 meters) high, according to the company. The seawall is planned between the sandhills and nuclear plant.
Trade Minister Banri Kaieda said the utility company should halt operating its nuclear reactors while implementing such safety measures.
"Until the company completes safety steps, it is inevitable that it should stop operating nuclear reactors," Kaieda said.
Shizuoka governor Heita Kawakatsu called the move "a wise decision."
"I pay my respect for the decision. We must do our utmost to secure alternative sources of energy," the governor said in a statement.
The plant serves around 16 million people in central Japan. Faced with a possible power crunch due to the shutdown, the prime minister sought public understanding.
"We will experience some power crunch for sure. But we can overcome this with public support and understanding," Kan said.
The region powered by the plant includes Aichi, where Toyota Motor Corp.'s headquarters and an auto plant are located.
The March 11 earthquake and tsunami damaged the Fukushima Dai-ichi nuclear plant, which lost its power and cooling systems, triggering fires, explosions and radiation leaks in the world's second-worst nuclear accident.
Radiation leaks from the Fukushima plant have forced 80,000 people living within a 12-mile (20-kilometer) radius to leave their homes. Many are staying in gymnasiums and community centers.
Residents in Shizuoka have long demanded suspension of the Hamaoka reactors.
Associated Press writer Mari Yamaguchi contributed to this report.