Masao Yoshida, 58, was at the power station on March 11, 2011, when towering waves swamped cooling systems and sparked meltdowns that released plumes of radiation.
Yoshida led the subsequent effort to get the crippled complex under control, as workers battled frequent aftershocks to try to prevent the disaster worsening.
Government contingency plans revealed after the event showed how scientists feared a chain reaction if Fukushima spiralled out of control, a scenario that could have seen other nuclear plants engulfed and would have meant evacuating Tokyo.
"He died of oesophagal cancer at 11:32 am today at a Tokyo hospital," said a spokesman for plant operator Tokyo Electric Power (TEPCO).
Yoshida left the plant soon after being suddenly hospitalised in late November 2011.
TEPCO has said his cancer was unlikely to be linked to radiation exposure in the months after the disaster.
The company has said it would take at least five years and normally 10 years to develop this particular condition if radiation exposure were to blame.
He was still employed by the company at the time of his death.
The disaster saw three reactors go into meltdown, spewing radiation into the air, sea and food chain in the worst nuclear accident since the 1986 Chernobyl disaster.
No deaths have been directly attributed to the radiation released by the accident, but it has displaced tens of thousands of people and left large areas of land uninhabitable, possibly for decades.
The plant itself remains fragile, with TEPCO struggling to deal with the tonnes of radioactive water left over from efforts to cool molten reactor cores.
Samples taken yesterday showed levels of possibly cancer-causing caesium-134 were more than 90 times higher than on Friday, at 9,000 becquerels per litre, TEPCO revealed.
Levels of caesium-137 stood at 18,000 becquerels per litre, 86 times higher than at the end of last week, the utility said.
Scientists say fully decommissioning the plant will take 30 to 40 years.
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