The district court in southern Kagoshima prefecture turned down the challenge by local residents who wanted to halt the refiring of the No. 1 and No. 2 reactors at the Sendai nuclear plant, a court official said.
They could come back online as early as this summer.
The ruling comes just over a week after another court in Fukui in central Japan sided with a citizens' group by temporarily halting the restart of the No. 3 and No. 4 reactors at the Takahama nuclear plant.
Top government spokesman Yoshihide Suga declined to comment on the latest court ruling.
But he said Tokyo stood behind an earlier decision by the Nuclear Regulation Authority to greenlight the restart of all four reactors because they met new, tougher standards.
"The government respects the decision made by the Nuclear Regulation Authority to resume plants that it considers meet safety standards, while placing the top priority on safety over any other factor," he told reporters at a regular press briefing.
The Kagoshima court ruled that Japan's new nuclear safety standards were not unreasonable, Jiji Press news agency and other media reported, contrary to the Fukui court which had said the standards "lacked rationality".
Kyushu Electric Power, the operator of the Sendai nuclear plant, said the latest judgement was "appropriate" as it accepted the company's opinion that the reactors' safety was assured.
Once-trusted nuclear has become the object of public suspicion since a tsunami smashed into the Fukushima plant in March 2011, sending reactors into a meltdown that left villages uninhabitable.
The lawyer acting for the plaintiffs in the most recent case said he was disappointed.
"I doubt the court properly looked at the true extent of the Fukushima accident's damage and horribleness," Hiroyuki Kawai told a press conference.
Japan's entire stable of nuclear reactors was gradually switched off following the Fukushima disaster, which forced tens of thousands of people from their homes.
Many are still displaced and some settlements may be uninhabitable for decades, scientists warn.
But pro-nuclear premier Shinzo Abe and the country's business sector have pushed to restart the plants that once supplied more than one quarter of Japan's electricity, as a plunging yen had sent energy import bills through the roof.
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