"This was a stupid act of intrusion, it's intolerable," EDF chief Henri Proglio said in the French city of Lyon.
EDF will "learn lessons and reinforce its anti-intrusion systems" to "ensure it's more difficult in the future" to break into nuclear facilities, he said.
On Monday, nine activists from the environmental group broke into the Nogent-sur-Seine plant near Paris and two into the Cruas plant in southern France in an action Greenpeace said was aimed at exposing the vulnerability of the facilities.
The 11 were arrested and are to face charges in court in January.
Proglio repeated EDF's assertion that it had immediately identified the intruders but did not move against them because it was clear they were not armed.
"No sensitive site was breached," he said.
France, the world's most nuclear-dependent country, relies on atomic power for 75 percent of its energy and operates 58 reactors.
But the country's reliance on nuclear power has been increasingly called into question since the Fukushima disaster in Japan, which prompted Germany to announce plans to shut all of its reactors by the end of 2022.