The Airbus A320 was en route from Paris to Cairo with 66 passengers and crew when it went down overnight.
Egyptian Vice-President Ahmed Adel told CNN that the rescue operation was “turning into a search and recovery”.
Officials say the plane was more likely to have been brought down by a terrorist act than a technical fault.
“There have been finds south-east of Crete, inside the Cairo flight information area,” Greek army general staff spokesman Vassilis Beletsiotis told AFP news agency.
The search in seas south of the Greek island of Karpathos involves Greek and Egyptian naval forces, and the British Royal Air Force.
Sixty-six people were on board Flight MS804, most of them from Egypt and France. A Briton was among the passengers.