TOKYO — On the evening of March 12, the Fukushima Daiichi nuclear plant’s oldest reactor had suffered a hydrogen explosion and risked a complete meltdown. Prime Minister Naoto Kan asked aides to weigh the risks of injecting seawater into the reactor to cool it down.

At this crucial moment, it became clear that a prime minister who had built his career on suspicion of the collusive ties between Japan’s industry and bureaucracy was acting nearly in the dark. He had received a confusing risk analysis from the chief nuclear regulator, a fervently pro-nuclear academic whom aides said Mr. Kan did not trust. He was also wary of the company that operated the plant, given its history of trying to cover up troubles.

Mr. Kan did not know that the plant manager had already begun using seawater. Based on a guess of the mood at the prime minister’s office, the company ordered the plant manager to stop.

But the manager did something unthinkable in corporate Japan: he disobeyed the order and secretly continued using seawater, a decision that experts say almost certainly prevented a more serious meltdown and has made him an unlikely hero.