A TEPCO official cited physicians as saying Kazuhiko Kokubo, 24, and Yoshiki Terashima, 21 had died of bleeding from multiple injuries.
The utility said their remains had been found last Wednesday in the reactor four turbine building of the Fukushima plant, where the tsunami knocked out cooling systems and sparked an emergency that has released high radiation.
Their bodies required decontamination from radioactive materials, and they were only formally declared as deceased on Saturday, it said.
TEPCO said in a statement: "We extremely regret losing the two young employees who tried to secure the safety of the plant while it was being hit by the quake and tsunami."
The crippled plant is continuing to release radiation into the air, ground and sea in Japan's worst ever nuclear crisis.