A science and technology ministry official said the non-radioactive accident, in which four workers were killed by escaping steam, was unrelated to the International Thermonuclear Experimental Reactor (ITER) bid.
"This is totally unrelated," Takashio Hayashi told AFP. "These are two completely separate things."
Seven workers were also injured, two critically, by super-heated steam when a pipe burst Monday in the turbine room of the Mihama Nuclear Power Plant in central Japan.
Japan and the European Union are vying to host the 10 billion dollar experimental test-bed for what is being billed as a clean, safe, inexhaustible energy source of the future, in a project that also includes China, Russia, South Korea and the United States.
The European bloc wants to host the project at the southern French town of Cadarache, near Marseille and has reportedly won support from China and Russia.
South Korea and the United States appear to prefer the Japanese site, in the northern village of Rokkasho-mura.
Dominique Ochem, the nuclear counsellor at the French embassy in Tokyo, also said the Mihama accident would have no bearing on the outcome of the competition to host ITER.
"I do not believe that this will prejudice the Japanese bid," he said.
The decision on the winner, which must be by consensus among the six partners, would be a "political decision, not scientific, and the partners are not ready to change their mind," Ochem said, referring to the deadlock in discussions.
The choice of the site must be made by consensus, and not by a simple majority, partly because all parties will be required to fund the reactor which will cost roughly five billion dollars to build and another five billion to run over 20 years.