With no bodies to bury, relatives and friends of some of the 66 people on board held special prayers for the lost.
But the mystery remained over why the Airbus A320 — which had been cruising normally in clear skies on a night flight from Paris to Cairo early on Thursday — suddenly lurched left and then right and plummeted into the sea, never issuing a distress signal.
Egyptian authorities said they believe it may have been an act of terrorism, as have Russian officials and some aviation experts, but so far no hard evidence has emerged.
No militant group has claimed to have brought down the aircraft.
That is a contrast to the downing of a Russian jet in October over Egypt’s Sinai Peninsula.
In that incident, which killed 224 people, the Islamic State’s branch in Sinai issued a claim of responsibility within hours.
Three European security officials said the passenger manifest for EgyptAir Flight 804 contained no names on terrorism watch lists.
The officials spoke on condition of anonymity as they were not authorised to discuss the investigation. The list was leaked online and has not been verified by EgyptAir.
Still, the tragedy has fuelled suspicions of terrorism, especially in light of the bombing of the Russian plane and the recent extremist attacks in Paris and Brussels.
Some aviation experts have said the circumstances suggest a bomb blast.
Experts said answers will come only with examination of the wreckage and the plane’s black box recorders.
But retrieving them may take time.
The water is 8,000 to 10,000 feet deep in the area where the jetliner is thought to have gone down, roughly halfway between Egypt’s coastal city of Alexandria and the Greek island of Crete.
The Egyptian army said it had found debris around 290km north of Alexandria, and that it was searching for more.
EgyptAir said luggage and seats were found, as well as body parts.
France, Greece, Italy, Cyprus, and Britain have joined the search, which encompasses a wide area south of Crete.
Investigators from Egypt, France, and Britain, as well as from Airbus, will examine everything found in the search, Egyptian officials said.
In Egypt — home to 30 of those on the flight — civil aviation minister Sherif Fathi informed relatives there were no survivors, the Al-Masry Al-Youm newspaper said.
In several mosques around the Egyptian capital, families and friends of the victims held what is known as “Salat al-Ghaib,” Arabic for “prayers for the absent”.
These are held for the dead when there is no body.
At the al-Thawra Mosque in Cairo’s Heliopolis district, mourners wept as they prayed for a family of four who were killed — Salah Abu Laban, his wife Sahar Qouidar, their son Ghassan Abu Laban, and daughter-in-law Reem al-Sebaei.
President Abdel-Fattah el-Sissi’s office issued a statement expressing its condolences to relatives and its “deep regret and sadness for the victims”. It added: “God give great mercy and host them in his heaven.”
The statement marked the first official recognition by Egypt’s government that the missing plane had crashed.
The crash has struck a demoralising blow to Egypt.
The economy has been gutted by years of turmoil since the 2011 overthrow of president Hosni Mubarak, and the Russian plane crash caused a new plunge in tourism, one of the country’s main money-makers.
Egyptian security officials said they were running background checks on the passengers to see if any had links to extremists.
French foreign minister Jean-Marc Ayrault said on France-2 television there is “absolutely no indication” of what caused the crash.
France’s junior minister for transport, Alain Vidalies, defended security at Paris’ Charles de Gaulle Airport.