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The order came as Kansai Electric Power Company (KEPCO) readied to refire a second reactor at the Oi plant, western Japan, just weeks after the first unit was restarted, ending a brief nuclear-free period in earthquake-prone Japan.
A spokesman for the Nuclear and Industrial Safety Agency said KEPCO had to re-examine the Earth's crust underneath Oi, while the operator of the Shika plant in nearby Ishikawa also had to carry out further studies.
The decision came after geological experts argued both plants are likely sitting on active faults and could be vulnerable to earthquakes if tectonic plates shift.
Japan's entire stable of nuclear reactors was shut down in the months after the disaster at Fukushima when an earthquake-sparked tsunami knocked out cooling systems causing meltdowns that spread radiation over a large area.
A parliamentary report earlier this month called for further research into the effect on the reactors of the earthquake itself, adding it was not possible to say for certain the tsunami was the sole cause of damage at Fukushima.
Despite widespread public fears over the safety of nuclear power, Prime Minister Yoshihiko Noda in June ordered the restarting of reactors at Oi amid fears of a summer power crunch.
Unit No. 3 was back up at full operating power by mid-July and KEPCO said its plans to re-fire Unit No. 4 on Wednesday would not be affected by the probe order.
"The company from its evaluations believes the fault has not been active for between 120,000 and 130,000 years," a spokesman said.
"Now the company has received the order to reinvestigate the matter and swiftly report, we will comply fully with this order," he said.
A statement from Hokuriku Electric Power Co, the operator of the Shika plant, said the company would fully comply with the order to conduct a survey and would report its findings to the safety agency.
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