An official investigative committee which made the discovery has referred the case to Egypt's state prosecution, it added in a statement.
The plane had been en route to Cairo from Paris when a fire broke out and it crashed into the eastern Mediterranean, investigators had previously said.
Under Egyptian law, the prosecution takes over "if it becomes clear to the investigative committee that there is criminal suspicion behind the accident", the ministry said.
EgyptAir MS804 was en route from Paris to Cairo when it disappeared from radar over the Mediterranean.
Investigators determined that a fire broke out in or near the cockpit of the Airbus A320 before it crashed between Crete and the coast of northern Egypt.
Egypt's aviation minister had said a terrorist attack was the most likely cause of the crash.
There were 66 people were on board: 56 passengers and 10 crew members consisting of two cockpit crew, five cabin crew, and three security personnel. There were no survivors. Fifteen French passengers were among the dead.
Two babies and one child were also among the passengers.
READ ALSO: What we know about EgyptAir flight MS804
France's air safety agency BEA and the plane manufacturer Airbus both declined to comment on Thursday's announcement, which comes while Cairo is still investigating the October 2015 crash of a Russian passenger plane in Egypt's Sinai.
The Islamic State group claimed responsibility for bombing the Airbus A321 Russian plane that crashed after takeoff from a Sinai resort headed for St Petersburg, killing 224 passengers and crew.
There has been no such claim linked to the EgyptAir crash.
Aviation experts have said there is little chance that a mechanical fault was responsible.
The plane only entered service in 2003, making it relatively new for an aircraft that tends to operate for 30 to 40 years.
The EgyptAir plane was flying at 37,000 feet (11,000 metres) and disappeared about 130 nautical miles off the Greek island of Karpathos.
The plane plunged 22,000 feet and swerved sharply before it disappeared from radar screens, Greece's Defence Minister Panos Kammenos said at the time.
If a bombing is established, investigators will have to determine if a device could have been smuggled aboard a flight taking off from France's busiest airport, Paris Charles de Gaulle.
Security has been tight since last year's jihadist attacks in the French capital.
Internet site FlightRadar24 indicates the EgyptAir plane travelled to Egypt, Tunisia and Eritrea in the two days before the crash, leaving open the possibility that a device could have been planted prior to its arrival in France.