Tokyo Electric Power Co. says in a statement that the plutonium was discovered Monday in five locations around the plant, which has been leaking radiation for nearly two weeks.
TEPCO official Jun Tsuruoka says the amounts were very small and were not a risk to public health.
Experts had expected traces of plutonium to be detected once crews began searching for it this week, since it is present in the nuclear fuel in the troubled complex.
TEPCO also said that water is testing 100,000 times normal amounts of radiation levels. Workers reportedly discovered radioactive water in the deep trenches outside three units, with the airborne radiation levels outside Unit 2 exceeding 1,000 millisieverts per hour - more than four times the amount that the government considers safe for workers.
Officials said the contaminated water in Unit 2 appears to be due to a partial meltdown of the reactor core.
The radioactive water inside several buildings at the six-unit plant must be eliminated before workers can continue to restore the plant's regular cooling system, which could take weeks.
The nuclear plant has been leaking radiation since a magnitude-9.0 quake on March 11 triggered a tsunami that engulfed the complex.
The frantic effort to get temperatures down and avert a widening disaster has been slowed and complicated by fires, explosions, leaks and dangerous spikes in radiation.
Meanwhile, Japan was hit with a magnitude-6.5 aftershock that briefly triggered another tsunami alert early Monday morning. There was no tsunami.
The final death toll from the disasters is expected to top 18,000, and hundreds of thousands remain homeless.
The Associated Press contributed to this report.