The passengers and crew were unharmed.
Eighty-one people, including 21 foreigners and 15 crew, were on board the Airbus 320, Egypt’s Civil Aviation Ministry said in a statement.
Conflicting theories emerged about the motives of the hijacker, an Egyptian. A senior Cypriot official said he seemed unstable and the incident did not appear related to terrorism. The Cypriot state broadcaster said he had demanded the release of women prisoners in Egypt.
In the midst of the hijack, witnesses said he threw a letter on the apron at Cyprus’s Larnaca airport, written in Arabic, and asked that it be delivered to his Cypriot ex-wife.
After the aircraft landed at Larnaca, negotiations began and everyone on board was freed except three passengers and four crew, Egypt’s Civil Aviation Minister Sherif Fethy said.
Soon afterwards, Cypriot television footage showed several people leaving the plane via the stairs and another man climbing out of the cockpit window and running off.
The hijacker then surrendered to authorities.
Cypriot Foreign Minister Ioannis Kasoulides said the hijacker had threatened to blow himself up and demanded that the aircraft be refueled and head to Istanbul.
“It looks like he realized his demands would not be met, allowing the last two hostages, Britons, to flee the aircraft. He also tried to leave, running out. He was arrested,” said Kasoulides.
“The explosives on him were examined. They weren’t explosives, but mobile phone covers.”
Egyptian Prime Minister Sherif Ismail said the hijacker would be questioned to ascertain his motives. “At some moments he asked to meet with a representative of the European Union and at other points he asked to go to another airport but there was nothing specific,” he said.
Watch footage of the man climbing out of the cockpit window:
Egypt’s Civil Aviation Ministry said the pilot, Omar al-Gammal, had told authorities that he was threatened by a passenger who claimed to be wearing an explosive belt and forced him to divert the plane to Larnaca.
Reached by telephone, Gammal told Reuters that the hijacker seemed “abnormal”. Sounding exhausted, he said he had been obliged to treat the man as a serious security threat.
Photographs on Egyptian state television showed a middle-aged man on a plane wearing glasses and displaying a white belt with bulging pockets and protruding wires.
Its over. The #hijacker arrested. #LarnacaAirport # Egyptair
— Cyprus MFA (@CyprusMFA) March 29, 2016
Television channels showed video footage of the hijacker, identified as Seif Eldin Mustafa, 59, being searched by security men at a metal detector at Borg al-Arab airport in Alexandria.
Interior Ministry officials said he was expelled from law school and had a long criminal record, including robberies.
Fethy, the Egyptian minister, said authorities suspected the suicide belt was not genuine but treated the incident as serious to ensure the safety of all those on board.
“We cannot say this was a terrorist act… he was not a professional,” Fethy told reporters after the incident.
EgyptAir delayed a New York-bound flight from Cairo onto which some passengers of the hijacked plane had been due to connect. Fethy said it was delayed partly due to a technical issue but partly as a precaution.
The hijacked plane remained on the tarmac at Larnaca throughout the morning while Cypriot security forces took up positions around the scene.
#BREAKING: all Egyptian passengers released from plane in #Cyprus: Foreign passangers still onboard pic.twitter长沙桑拿按摩论坛,/3JgoaWflU9
— Amichai Stein (@AmichaiStein1) March 29, 2016
The incident will deal another blow to Egypt’s tourism industry and hurt efforts to revive an economy hammered by political unrest following the 2011 uprising that ousted veteran ruler Hosni Mubarak.
The sector, a main source of hard currency for the import-dependent county, was already reeling from the crash of a Russian passenger plane in the Sinai peninsula in late October.
President Abdel Fattah al-Sisi has said the Russian plane was brought down by a terrorist attack. Islamic State has said it planted a bomb on board, killing all 224 people on board.
The latest incident raised renewed questions over airport security, though it was not clear whether the hijacker was even armed. Ismail said stringent measures were in place.
Passengers on the plane included eight Americans, four Britons, four Dutch, two Belgians, an Italian, a Syrian and a French national, the Civil Aviation Ministry said.
Cyprus has seen little militant activity for decades, despite its proximity to the Middle East.
A botched attempt by Egyptian commandos to storm a hijacked airliner at Larnaca airport led to the disruption of diplomatic relations between Cyprus and Egypt in 1978.
In 1988, a Kuwaiti airliner which had been hijacked from Bangkok to Kuwait in a 16-day siege had a stopover in Larnaca, where two hostages were killed.
Negotiations with the Hijacker result in the release of all the passengers, except the crew and four foreigners.
— EGYPTAIR (@EGYPTAIR) March 29, 2016