All hostages held on the plane during the siege at Larnaca Airport were released just before 1pm (GMT).
The aircraft, which was en route from Alexandria to Cairo and carrying 81 passengers, was forced to divert after the pilot was threatened by El Din Mustafa who claimed to be wearing a suicide belt.
In a tweet the Cypriot foreign ministry confirmed the hijacker had been detained.
https://twitter.com/CyprusMFA/status/714779614476763136?lang=en-gb
The motive behind the hijacking remains unclear although some reports say El Din Mustafa wanted to talk to his estranged Cypriot wife, while others believe he was seeking the release of female prisoners in Egypt.
Upon landing, he held crew and three foreigners hostage on the plane, although other passengers were released.
During the incident, Cypriot president Nicos Anastasiades said the situation was not terror related. He added: "We are doing our utmost in order for everyone to be released and safe and to give an end to this unprecedented incident."