EgyptAir Flight MS181 was taken over by a passenger claiming to be wearing a suicide explosive belt.
Airline officials later said they had been told by Cypriot authorities that the belt was fake.
The hijacker’s motives remain unclear but Cyprus President Nicos Anastasides said the incident was not terrorism-related.
No-one was injured in the hijacking, Cypriot government spokesman Nikos Christodulides tweeted.
After a morning of tension, the hijacker was seen walking down aircraft steps at Larnaca airport with his hands raised.
Some reports said the Egyptian man – named by Cypriot officials as Seif Eldin Mustafa – wanted to talk to his estranged Cypriot wife who lives on the Mediterranean island, while others said he was seeking the release of female prisoners in Egypt.
The hijacker’s surrender came shortly after several people were seen fleeing the aircraft. One – apparently a crew member – escaped by climbing out of the aircraft’s cockpit window.
In a tweet, the Cypriot foreign ministry confirmed the end of the crisis: “It’s over. The hijacker arrested.”
Throughout the morning, passengers had been seen leaving the aircraft after appearing to have been released.
Local media reports said the hijacker had handed over a four-page letter in Arabic after the plane landed at Larnaca in the morning, and that later a woman thought to be his wife had arrived at the airport.
Earlier, President Nicos Anastasiades had responded to a reporter’s question about whether the hijacker was motivated by romance, by laughing and saying: “Always there is a woman involved.”
EgyptAir said the Airbus A320 was carrying 56 passengers from Alexandria to Cairo, along with six crew members and a security official. It had initially said 81 passengers were on board.
A statement from Egypt’s civil aviation ministry said 26 foreign passengers were on board, including eight Americans, four Dutch citizens, four Britons, two Greeks, two Belgians, a French national, an Italian and a Syrian.
Larnaca airport, on the south coast of Cyprus, has been closed and scheduled flights diverted elsewhere.
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