The Egyptian civil aviation ministry initially said Greek authorities had found "floating material" and life jackets likely to be from the plane, an Airbus A320. Greek defence sources told Reuters the material was discovered in the sea 230 miles (370 km) south of the island of Crete.
However, late on Thursday EgyptAir Vice President Ahmed Adel told CNN that the wreckage had not been found.
"We stand corrected on finding the wreckage because what we identified is not a part of our plane. So the search and rescue is still going on," Adel said.
An official from the Egyptian civil aviation ministry said Egypt, Greece, and France were all involved in the search for the plane.
Egyptian President Abdel Fattah al-Sisi ordered the civil aviation ministry, the army's search and rescue centre, the navy, and the air force to take all necessary measures to locate debris from the aircraft.
In a statement issued by his office, Sisi also ordered an investigative committee formed by the civil aviation ministry to immediately start investigating the causes of the plane's disappearance.
Egyptian Prime Minister Sherif Ismail said it was too early to rule out any explanation for the crash, including an attack like the one blamed for bringing down a Russian airliner over Egypt's Sinai Peninsula last year. The country's aviation minister said a terrorist attack was more likely than a technical failure.
Officials from multiple U.S. agencies told Reuters that a U.S. review of satellite imagery so far had not produced any signs of an explosion aboard the EgyptAir flight.
The U.S. officials, who spoke on condition of anonymity to discuss intelligence matters, said the conclusion was the result of a preliminary examination of imagery and cautioned against media reports suggesting the United States believed a bomb was responsible for the crash.
They said the United States has not ruled out any possible causes for the crash, including mechanical failure, terrorism or a deliberate act by the pilot or crew.
Noteworthy that the aircraft pilot has 6275 of flying hours including 2101 flying hours on Airbus 320.
Greece had deployed aircraft and a frigate to search for the missing plane. Egypt said it would lead the investigation and France would participate. Paris said three investigators would arrive in Egypt on Thursday evening.
In Washington, President Barack Obama received a briefing on the disappearance from his adviser for homeland security and counter-terrorism, the White House said. A White House spokesman said it was too early to know the cause of the crash and offered condolences.
In its first admission that those on board the plane had died, EgyptAir said in a statement on Twitter, "EgyptAir expresses condolences to the families of the plane's victims and expresses its deep sorrow over this tragic accident. The company affirms it will take all measures to handle the situation and will conduct a comprehensive investigation."
Greek Defence Minister Panos Kammenos said the Airbus swerved 90 degrees to the left, spun through 360 degrees to the right and plunged from 37,000 feet to 15,000 before vanishing from Greek radar screens.
According to Greece's civil aviation chief, calls from Greek air traffic controllers to flight MS804 went unanswered just before it left Greek airspace, and it disappeared from radar screens soon afterwards.
There was no official indication of a possible cause, whether technical failure, human error or sabotage. Ultra-hardline Islamists have targeted airports, airliners and tourist sites in Europe, Egypt, Tunisia and other Middle Eastern countries over the past few years.
Asked if he could rule out terrorist involvement, Ismail told reporters: "We cannot exclude anything at this time or confirm anything. All the search operations must be concluded so we can know the cause."
French President Francois Hollande also said the cause was unknown. "No hypothesis can be ruled out, nor can any be favoured over another."
The aircraft was carrying 56 passengers - with one child and two infants among them - and 10 crew, EgyptAir said. They included 30 Egyptian and 15 French nationals, along with citizens of 10 other countries.
The Canadian government said on Thursday that two Canadian citizens were aboard and Foreign Affairs Minister Stephane Dion said Canadian officials were working with authorities to confirm if any other Canadians were on the flight.
The U.S. State Department said there was no indication that American citizens were on board.