A submarine that could operate at a depth of 3,000 metres under sea level had been deployed for the purpose, Sisi said in a televised address.
"This (submarine) moved today in the direction of the plane crash because we are working hard to retrieve the two boxes, which are the black boxes," he said, adding: "All the theories are possible."
Sisi's remarks came a day after French authorities said "all theories are being examined and none is favoured".
Investigators continued to piece together clues for a potential breakthrough even as some reports of release of audio from the jet and even of locating the black boxes emerged.
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Multinational searchers scouring the Mediterranean waters have made headway by recovering debris, passengers' belongings, body parts, luggage and aircraft seats from the jet, that initially went 'missing' and was later declared crashed.
Egypt's military displayed wreckage and personal belongings yesterday. The chunks of debris included an uninflated life vest, a seat, a purse, shoes, carpet, a scarf, parts of chairs and cushions and a sling bag. The EgyptAir label appeared on one piece of wreckage.
"The search is ongoing. It has uncovered initial pieces of the aircraft, body parts, belongings of the deceased, and it will continue hopefully until we can ascertain exactly where the plane has gone down," Egyptian Foreign Minister Sameh Shoukry said.
Shoukry, meanwhile, told CNN that it was not clear how long the searchers will take to recover the cockpit voice and flight data recorders - the so-called black boxes - to shed crucial information about what was going on during the plane's final moments.
"We do not, I think, have the technical abilities to operate in such deep waters, whereas many of our partners might have this facility," he said, referring to the US, France, Britain, Russia and others cooperating in the search.