Prime Minister Naoto Kan said the measure was to ensure safety, citing experts' forecast of a 90 per cent probability of a major quake striking the central region within 30 years.
The government has asked operator Chubu Electric Power Co. to suspend two running reactors and a third shut for a regular inspection at its coastal Hamaoka nuclear plant in Shizuoka, west of Tokyo.
If an accident occurs at Hamaoka, it could create serious consequences, Kan said.
Kan said the safety measure was made after the radiation crisis at the Fukushima Dai-ichi nuclear plant, which was crippled by an earthquake and tsunami March 11 that also left more than 25,000 people dead and missing on the northeast coast.
The Fukushima Dai-ichi nuclear plant 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 20-kilometre radius to leave their homes. Many are staying in gymnasiums and community centres.
Residents in Shizuoka have long demanded suspension of the Hamaoka reactors.