The last communications from the aircraft prior to its submersion were two transmissions from its emergency locator transmitter that were received by the International Cospas-Sarsat Programme.

Nearly four weeks after the crash, several main sections of wreckage were identified on the seabed, and both flight recorders were recovered in a multinational search and recovery operation.

Egypt's Civil Aviation Authority, which headed the investigation, concluded that the crash was the result of an explosion occurring in the galley near the cockpit, which was rapidly engulfed by smoke and fire, exacerbated by oxygen flow being present.

[16][17] It disappeared from radar while flying at flight level 370 (about 37,000 ft (11,300 m) in altitude) in clear weather, 280 km (170 mi; 150 nmi) north of the Egyptian coast,[18] and about the same distance from Kastellorizo, over the eastern Mediterranean on 19 May at 02:30.

It was originally reported that a distress signal from emergency devices was detected by the Egyptian military at 04:26, two hours after the last radar contact; officials later retracted this statement.

[24][25] This information was initially rejected on 23 May by an Egyptian official from the National Air Navigation Services Company, who stated that there was no change in altitude and no unusual movement before the aircraft disappeared from radar.

[32][33] On 20 May, units of the Egyptian Navy and Air Force discovered debris, body parts, passengers' belongings, luggage, and aircraft seats at the crash site, 290 km (180 mi; 160 nmi) off the coast of Alexandria, Egypt.

[37][38][39] The U.S. National Oceanic and Atmospheric Administration confirmed that the emergency locator transmitter signal was received by satellites minutes after the airliner disappeared from radar.

[41][42] At the beginning of June, after ultrasonic pulses from a ULB of one of the flight recorders had been detected, a "priority search area" 2 kilometres (1 mi) in radius[43] was established.

[44][45] The John Lethbridge,[46] a vessel belonging to Deep Ocean Search,[44] equipped with a remotely operated underwater vehicle that can detect signals in depths of up to 6,000 metres (20,000 ft), and map the seabed, was contracted by Egyptian authorities.

[28] On 15 June, Egyptian authorities announced that searchers on board the John Lethbridge had identified several main sections of wreckage on the seabed.

On arrival, the recovered remains were transferred from the John Lethbridge to Egypt's Department of Forensic Medicine in Cairo for DNA analysis and processing.

[53] On 22 May, an Egyptian remotely operated underwater vehicle (ROV), owned by the country's Oil Ministry, was deployed to join the search for the missing aircraft.

[54][55][56] According to Egypt's chief investigator with the Civil Aviation Ministry, Ayman al-Moqadem, the ROV cannot detect signals from flight recorders.

[57] A French Navy D'Estienne d'Orves-class aviso ship, the Enseigne de vaisseau Jacoubet, equipped with sonar able to detect the underwater "pings" emitted by the ULBs of the flight recorders, arrived at the possible crash site on 23 May.

[34][58] The French ship can deploy an ROV that can dive up to 1,000 metres (3,300 ft) and that is able to detect signals from ULBs but with limited depth range.

[50] On 16 June, Egyptian authorities announced that the searchers on the John Lethbridge had found the cockpit voice recorder (CVR), damaged, at a depth of 13,000 feet (4,000 m).

[71] On 27 June, the BEA announced that the FDR had been repaired and sent back to Cairo for data analysis by civil aviation safety authorities.

[76][77] This information was later denied on 23 May by an Egyptian official from the National Air Navigation Services Company, who stated there was no change in altitude and no unusual movement before the aircraft disappeared from radar.

[78] Shortly after the disappearance, the French government began to investigate whether there had been a security breach at Paris Charles de Gaulle Airport.

[79][81] Smoke detectors of the type installed on the aircraft can also be triggered by the condensation of water vapour, producing fog, in the event of a sudden loss of pressure inside the cabin.

[87][88][89] Aviation expert David Learmount of Flight International suggested that an electrical fire could have started in the aircraft's avionics compartment[90] and that the aircrew may have been too distracted to communicate their distress to air traffic control.

[91] On 22 May, the French television station M6 reported that, contrary to official statements, one of the pilots told Cairo air traffic control about smoke in the cabin, and decided to make an emergency descent.

[95] At the beginning of June, France 3 and Le Parisien reported that the aircraft had performed three emergency landings in the hours before the crash—at Asmara, Tunis, and Cairo—followed by technical inspections, after ACARS messages "signalled anomalies on board shortly after takeoff from three airports".

[109][110] On 13 January 2017, French newspaper Le Parisien published an article claiming that unspecified "French authorities" believed the aircraft might have been brought down by a cockpit fire caused by an overheating phone battery; it noted parallels between the position where the co-pilot had stowed his iPad and iPhone 6S and data that suggested an accidental fire on the right-hand side of the flight deck, next to the co-pilot.

[113][114] A study conducted by the BEA found that "no evidence from the CVR confirms or refutes the hypothesis that people were smoking in the cockpit" and that "tests carried out do not suggest that a lit cigarette contributed to the accident sequence".

[115]: 40 On 30 October 2024, Egypt's Civil Aviation Authority concluded in its final report that the crash was the result of an explosion in the galley area behind the cockpit.