The hijacker, who was later identified as an Egyptian man, apparently had a suicide belt with which he threatened the plane's pilot.
The Airbus flight number MS181 had 55 passengers on board and was flying on a regular route when the hijacking took place, the Egyptians said. Egyptian state television said there was a lone hijacker and identified him as Ibrahim Samaha. It gave no further details.
Details were sketchy and the hijacker's motives were also not known, but an Egyptian Aviation Ministry statement said the "hijacker" threatened that he had a belt of explosives, the weapon of choice for Islamic militants in the Middle East.
Shortly after the hijacking, the plane landed at the airport in the southern Cypriot city of Larnaca, also on the Mediterranean. Cypriot officials said there were suspicions of a bomb on board.
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Initially a second Cypriot official said there "seems like there's more than one hijacker" and that there were no other demands made expect that police vehicles move away from the aircraft. All the officials in Egypt and Cyprus spoke on condition of anonymity because they were not authorised to speak to the media.
All 224 people on board were killed in the crash. Russia later said an explosive device brought down the aircraft and the extremist Islamic State group said it downed the plane.