President Abdel-Fattah el-Sissi also said Egypt was jointly investigating the Thursday crash with the French government. "It is very, very important to us to establish the circumstances that led to the crash of that aircraft," he said in comments broadcast live on Egyptian TV channels.
PHOTOS: EgyptAir flight crashes in Mediterranean
He said the submarine, which has the capacity to operate at a depth of 3,000 meters (9842 feet) below the surface, left for the site Sunday. He gave no further details.
Making his first public comments since the crash of the Airbus A320 while en route from Paris to Cairo, el-Sissi says it "will take time" to determine the exact cause of the crash, which killed all 66 people on board.
He thanked the nations that have joined Egyptian navy ships and aircraft in the search for the wreckage and started his comments with a minute of silence in remembrance of the victims.
El-Sissi also cautioned the media against premature speculation on the cause of the crash.
"There is not one scenario that we can exclusively subscribe to ... all scenarios are possible," he said.
El-Sissi spoke a day after the leak of flight data showing trouble in the cockpit and smoke in a plane lavatory aboard the doomed aircraft, bringing into focus the chaotic final moments of the flight, including a three-minute period before contact was lost as alarms on the plane screeched one after another.
Officials have been cautioning that it was still too early to say what happened to the aircraft, but mounting evidence points to a sudden, dramatic catastrophe that led to the crash.
Egypt's military on Saturday released the first images of aircraft debris plucked from the sea, including personal items and damaged seats. Egypt is leading a multi-nation effort to search for the plane's black boxes and other clues that could help explain its sudden plunge into the sea.
"If they lost the aircraft within three minutes that's very, very quick," said aviation security expert Philip Baum. "They were dealing with an extremely serious incident."
Authorities say the plane lurched left, then right, spun all the way around and plummeted 38,000 feet (11,582 meters) into the sea - never issuing a distress call.
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. Beside Egypt, ships and planes from Britain, Cyprus, France, Greece and the United States are taking part searching a wide area of sea 180 miles (290 kilometers) north of the Egyptian port city of Alexandria.
The EgyptAir tragedy deepens the country's struggle to revive its battered economy. While it may not reflect directly on security at Egypt's airports - which has been under international scrutiny since a Russian airliner crashed in the Sinai Peninsula in October after taking off from an Egyptian resort - the country's association with yet another air disaster will further damage its vital but currently depressed tourism industry.