The company described the low-level flyover, which occurred at about 5.30 a.m. on June 5, as another act of nuclear terrorism by Russia.
"To date, Russia continues to pose a threat to the nuclear safety of Ukrainian NPPs and threatens the world with a new nuclear catastrophe," Energoatom said.
"The 'Rashists' (Russian fascists) still don't understand that even the smallest fragment of a missile, if it hit a working reactor, might cause a nuclear disaster and radiation leak."
This is not the first time Russia has fired cruise missiles right over a Ukrainian nuclear power plant.
Just over a month ago, on April 26, two Russian cruise missile flew at low altitude over the Zaporizhzhya Nuclear Power Plant in Enerhodar, Zaporizhzhya Oblast, on their way to strike targets in Zaporizhzhya.
Energoatom at that time also warned of the dangers of flying cruise missiles at such low altitude over operating nuclear reactors.