It says there are 59 passengers and 10 crew members on board Flight MS804.
The aircraft was flying at 37,000ft (11,300m) when it went missing over the eastern Mediterranean. An official said the plane lost contact with radar at 02:45 Cairo time (00:45 GMT).
The company said it would issue an update “when more information becomes available”.
EgyptAir said the plane disappeared about 10 miles (16km) into Egyptian air space.
It said the concerned authorities had been notified, and search and rescue teams were now looking for the plane.
According to the flightradar24.com website, which tracks passenger flights around the globe, the plane is an Airbus A320.