The meat is reported to have come from one of 11 cows shipped this month to Tokyo from a farmer in Minamisoma city.
The cows, which were raised and shipped just outside of the 20-kilometre no-go zone around the plant, all showed high levels of radioactive caesium,ranging from 1,530 to 3,200 becquerel per kilogram, compared with the legal limit of 500.
According to a Tokyo official, it was the first time excessive levels of radioactive caesium have been found in meat.
Greenpeace Japan executive director Junichi Sato says the incident shows the Japanese government is incapable of controlling contamination of caesium and radioactive material.
"The government has to take a more cautious approach not to release any contaminated food to the market. The only way not to have these kind of terrible stories is not to send out food from that region," he said.
Following the latest inspection results, the government of Fukushima prefecture immediately requested that the city of Minamisoma refrain from shipping cows and beef.
Fukushima prefecture has checked radiation levels of the outer skin of all livestock shipped from areas near the troubled nuclear plant, and the 11 cows had cleared external inspection.
The city of Minamisoma lies on the outskirts of the Fukushima Daiichi nuclear power plant, which has leaked radioactive substances into the environment after the 11 March tsunami and earthquake crippled its cooling systems.