Local residents lost their bid for an injunction to block the refiring of the No.3 and No.4 reactors at the Genkai nuclear plant in southwestern Japan on safety grounds, according to a district court official.
The site, operated by Kyushu Electric Power, lies some 100 kilometres (62 miles) north of Kumamoto prefecture which was hit by a deadly earthquake last year.
Residents unsuccessfully argued that the utility had not taken enough measures to prevent an accident linked to a natural disaster.
The restarts are not likely to happen for at least several months.
The court ruling comes a week after another utility switched on a reactor at the Takahama plant in Fukui prefecture, some 350 kilometres (215 miles) west of Tokyo, bringing the number of running reactors in Japan to five.
Dozens more in the country still remain offline.
It was the world's worst nuclear accident since Chernobyl in 1986.
Since then, just a handful of reactors have come back online due to public opposition and as legal cases work their way through the courts.
However, Prime Minister Shinzo Abe has aggressively promoted nuclear energy, calling it essential to powering the world's third-largest economy.
Much of the public remains wary of nuclear power after the disaster at Fukushima spewed radiation over a large area and forced tens of thousands to leave their homes, with some unlikely to ever return.
Last week, Japan's nuclear energy agency said five employees were exposed to dangerously high levels of radiation after a bag containing plutonium broke apart during a routine inspection.
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