An official with the health ministry said the ex-employee, who was in his thirties while working at the plant following the 2011 crisis, has developed leukaemia. He is now 41 years old, local media reported.
Japan nuclear plant begins post-Fukushima commercial operations
"The case has met the criteria" to link his illness to the accident, the official told a Tokyo press briefing, adding that other possible causes have been ruled out.
The man will be awarded compensation to pay for his medical costs and lost income, the official said, without elaborating on the amount.
Three similar cases of cancer in plant workers are still pending confirmation of a link to the accident.
There has been hot debate about whether the accident Fukushima would lead to a spike in cancer among employees of the plant and those who lived in the surrounding area.
The announcement on Tuesday will likely further inflame widespread public opposition to nuclear power, and comes less than a week after Japan restarted a second nuclear reactor following a shutdown of all plants after by the Fukushima crisis.
No deaths have been directly attributed to the radiation released during the 2011 accident, but it has displaced tens of thousands of people and left large areas of land uninhabitable, possibly for decades.
Japan lifts evacuation order for radiation-hit Fukushima town
A huge quake-sparked tsunami, which levelled Japan's northeast cost and killed more than 18,000 people, swamped cooling systems at the plant, sending some reactors into meltdown and sparking a decades-long clean-up.
Radiation was released into the air, sea and food chain in the worst nuclear accident since the 1986 Chernobyl disaster.
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