For the first time, the company, also known as Tepco, admitted there were clear internal regulations stating when a meltdown should be declared - when damage to the reactor core exceeds 5%.
The company told Japanese authorities that damage to one of the reactor cores had already passed 50% three days after the disaster, but continued to deny it publicly for two months.
Tepco says it will investigate why the procedures were not followed.
The meltdown at Fukushima in March 2011 happened because the plant lost power after it was swamped by the tsunami. It lost the ability to cool the nuclear reactor, leading to an explosive build-up of heat and gas.
It was the worst nuclear accident since the Chernobyl disaster in 1986.
Some 160,000 people were evacuated from the surrounding areas in the following weeks, and continuing high radiation levels mean most have never been able to return home.
Japan gradually shut down all the country's nuclear plants after the disaster. Three reactors have now been restarted under new safety rules, despite strong public unease - two in Sendai and one in Takahama.