The carrier released a statement saying Flight MS804, operating an Airbus A320, took off from Charles de Gaulle airport at 11:09 p.m. with 56 passengers, 7 crew and 3 security personnel.
The airline has said in its previous statement that the total people aboard were 69. The aircraft went missing at about 2:45 a.m. Cairo time, and search and rescue operations were under way in the Mediterranean Sea, a spokeswoman and the nation's civil aviation ministry said.
"EGYPTAIR has contacted the concerned authorities and bodies and inspection is underway through the rescue teams," the airline tweeted.
At Athens airport, Air-traffic controllers tried several times to contact the captain, but they failed to get a response, state-run Ahram Gate news website reported. Passengers on board were citizens of Egypt, France, Saudi Arabia and the U.K., Amr Zidan, a security official at Cairo Airport, said by phone.
The Flight MS804 took off from Europe and authorities there have been on high alert since terror attacks in Paris and Brussels.