The search came as there was worldwide concern about what caused the Airbus A320 aircraft to twist violently and plummet into the sea as it entered Egyptian airspace during a predawn flight from Paris, killing all 66 passengers and crew.
The cause of the crash remains a mystery but Egypt's civil aviation minister has said the possibility of a terror attack was stronger than technical failure.
The spokesman said it was "far too soon to interpret and understand the cause of Thursday's accident as long as we have not found the wreckage or the flight data recorders".
The submarine, which belongs to Egypt's Oil Ministry, is capable of going 9,842 feet under the water and will be used to search for the plane's black boxes, AP said.
The official was not authorised to discuss the investigation and spoke on condition of anonymity.
Investigators have been poring over the plane's passenger list and questioning ground crew at Paris' Charles de Gaulle airport, where the airplane took off.
More than 100 pieces of debris from EgyptAir Flight 804, which crashed into the Mediterranean Sea, has been found and reported to Egyptian officials, the U.S. Navy said today.
The Oil Ministry's submarine is capable of operating almost two miles deep where the plane went down in the Mediterranean Sea about 180 miles from the Egyptian coast.
Egypt's navy, with help from French and other vessels, was searching an area north of Alexandria, just south of where the signal from the plane was lost early on Thursday. Mohammed Samir said Saturday he had no information to share on the location or the retrieval of the black boxes.
"All hypotheses are possible", he said.
No group has claimed to have brought down the aircraft.
Data published by an aviation industry website appears to show automatic transmissions from the plane in the minutes before it crashed, indicating there was smoke onboard, though experts say the smoke alarms could also have been triggered by a sudden loss of pressure.
That is a contrast to the downing of a Russian jet in October over Egypt's Sinai Peninsula that killed 224 people.
Sissi cautioned that clear answers could take "a lot of time" and urged people not to speculate about the causes of the crash.
In the meantime, he said, "I tell Egyptian and foreign media not to rule out any hypotheses".