Workers discovered flames licking at piles of cardboard boxes placed near an incineration facility shortly before 1:00 pm (0400 GMT), Tokyo Electric Power Co said.
The fire damaged an area of about four metres by two metres, but was put out in a hour, it said.
The fire did not affect radiation levels in the plant, and no one was injured, it said.
TEPCO has struggled with a growing catalogue of incidents at the plant including several leaks of radioactive water, more than two years after the worst nuclear disaster in a generation.
Improvised fixes put in place since the disaster leave it vulnerable to problems and at the mercy of nature, with no immediate end in sight, critics say.