About 3,800 claimants in the suit, hailing from Japan and 32 other countries including the United States, Germany and South Korea, had sought largely symbolic compensation from the nuclear power plant manufacturers.
Under Japanese liability law, nuclear plant providers are usually exempt from damage claims in the event of an accident, leaving operators to face legal action.
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But the Tokyo District Court ruled that the law "is not unconstitutional", according to lawyers for the plaintiffs.
"We knew it was difficult to win under the current legal system in Japan, but it's clearly wrong that nuclear (plant) manufacturers don't have to bear any responsibility for an accident," Masao Imaizumi, 73, one of plaintiffs, told AFP.
"If they are spared responsibility, it could lead to disregard for product quality," he said, adding that the plaintiffs will appeal.
Toshiba welcomed the decision.
"The company recognises the verdict as an appropriate ruling handed out by the court," it said in a statement.
Hitachi and GE's Japan office could not be reached for comment.
Japan's Jiji Press also reported that the suit was rejected.
The suit — which sought just 100 yen (96 US cents) per claimant — was the first to be brought against nuclear power-plant suppliers over the accident, Akihiro Shima, lead lawyer for the plaintiffs, said previously.
The suit was first filed in January 2014 with just over 1,000 claimants, but more joined which saw the number nearly quadruple.
The plaintiffs had alleged that the companies failed to make necessary safety updates to the Fukushima reactors, swamped on March 11, 2011 by a magnitude 9.0 earthquake- sparked tsunami that lead to the worst nuclear accident since Chernobyl in 1986.
Embattled plant operator Tokyo Electric Power is already facing massive lawsuits and compensation costs.
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