An employee confirmed smoke was pouring from the roof of the number-four reactor at the plant, a TEPCO spokesman told reporters.
"We immediately informed local authorities and the fire department about it," the spokesman said. "We are battling the fire now."
A blaze and explosion hit the same reactor yesterday, causing a crack in the roof. The government has separately reported apparent damage to part of the container shielding the number-two reactor at Fukushima 250 kilometres northeast of Tokyo.
Japan is frantically working to avert a nuclear meltdown after Friday's massive earthquake and tsunami cut power to the ageing plant and knocked out cooling systems.
On Saturday an explosion blew apart the building surrounding the plant's number-one reactor but the seal around the reactor itself remained intact, officials said.
On Monday, shortly after Prime Minister Naoto Kan said the plant was still in an "alarming" state, a blast at its number-three reactor shook the facility, injuring 11 people and sending plumes of smoke billowing into the sky.
Late Monday TEPCO said fuel rods at the number-two reactor were almost fully exposed after a cooling pump there temporarily failed.