"They did not radio for help or lose altitude. They just vanished," the head of Egypt's air navigation authority Ehab Mohy el-Deen told the New York Times.
There were no reports of stormy weather at the time with authorities exploring the possibility that it was a terror attack.
The plane's erratic course suggested a number of possible explanations, including a catastrophic mechanical or structural failure, a bombing, or a struggle over the controls with a hijacker in the cockpit.
Yesterday there were unconfirmed reports that a merchant ship saw an "explosion that lit up the sky" near the Greek island of Karpathos where the plane was believed to have disappeared, according to the Wall Street Journal.
EgyptAir pointed out that the pilot was very experienced with 6275 hours flying experience, including 2101 hours flying the same model aircraft, which was an Airbus A320 manufactured in 2003. The co-pilot had 2766 hours flying time.
Egyptian Civil Aviation Minister Sherif Fathi said the disaster was still under investigation but said the possibility it was a terror attack "is higher than the possibility of having a technical failure".
Alexander Bortnikov, chief of Russia's top domestic security agency, went further, saying: "In all likelihood it was a terror attack."
Islamic State released a chilling video just days which directly threatened France but there has been no immediate claim from militants that they downed the plane.
If it was terrorism, it would be the second deadly attack involving Egypt's aviation industry in seven months.
Last October, a Russian passenger plane that took off from an Egyptian Red Sea resort crashed in the Sinai, killing all 224 people aboard. Russia said it was brought down by a bomb, and a local branch of the Islamic State claimed responsibility.
Authorities have been searching for the wreckage of the plane in the Mediterranean Sea, with efforts focused near Karpathos Island.