A tweet on the airline's official account said flight MS804 left Paris at 23:09 pm local time (0239 IST), "heading to Cairo (and) has disappeared from radar".
Further tweets in Arabic said contact was lost at 02:45 Cairo time, when the plane was just inside Egyptian airspace and at an altitude of 37,000 feet (11,000 metres).
There were 59 passengers and 10 crew aboard, according to the airline.
"EGYPTAIR has contacted the concerned authorities and bodies and inspection is underway through the rescue teams," another tweet in English said.
He surrendered after a six-hour airport standoff, which ended peacefully.
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