Workers have been struggling to bring the radiation leaking plant under control since the massive magnitude-9.0 earthquake and tsunami.
Tokyo Electric Power Co.'s spokesman said the smoke was seen rising from the area of the spent fuel storage pool at the plant's Unit 3 reactor building.
But despite the latest incident, the U.S. nuclear regulators say the containment of three reactors is intact.
"Today, all three units appear to be in a stabile condition," said Bill Borchardt, the Nuclear Regulatory Commission's executive director for operations.
A report by Japan's nuclear safety agency shows the plant failed to do equipment inspections at the Fukushima Dai-ichi nuclear plant in the weeks before the March 11 disasters. Among the machinery not inspected were the backup generators and parts of the cooling system that later led to the plant's overheating.
Nuclear safety officials have declined to say that the violations cited in the report or the location of the backup generators contributed to the current crisis.
Japanese officials had reported some progress over the weekend in their battle to bring the plant under control. But there also were hitches, including an unexpected surge in pressure in the reactor core at the troubled Unit 3.
And the nuclear crisis was far from over, with the discovery of more radiation-tainted vegetables and tap water adding to public fears about contaminated food and drink.
The World Health Organization said Monday that Japan needs to act quickly and ban food sales from areas around the damaged nuclear plant if the food there is found be contaminated.
The agency said radiation in food can accumulate in the body and poses a greater risk to health than radioactive particles in the air, which disperse within days.
Meanwhile, officials now estimate the death toll from the quake and tsunami will exceed 18,000.
The World Bank said the disasters have caused as much as $235 billion worth of damage and it may take five years to rebuild.
The bank said it will likely reduce half a percentage point from the country's economic growth this year. It said growth will pick up once reconstruction efforts accelerate.
The Associated Press contributed to this report.