The Larnaca court ordered an eight-day detention for Seif Eldin Mustafa.
Possible charges include air piracy, kidnapping and threatening behavior.
Seif Eldin Mustafa did not speak, but gave a victory sign as he was driven away by police. Cypriot authorities have described him as “psychologically unstable”, saying the incident was not terrorism-related.
EgyptAir flight MS181 was carrying 56 passengers from Alexandria to Cairo, along with six crew and a security official, when it was diverted to Cyprus.
During a stand-off lasting more than six hours, almost all passengers and crew were freed unharmed as authorities negotiated with Seif Eldin Mustafa.
One person, apparently a crew member, climbed out of a cockpit window, minutes before the suspect walked calmly out of the plane to surrender.
Cypriot Foreign Minister Ioannis Kasoulides said Seif Eldin Mustafa had initially asked to speak with his Cypriot ex-wife, who was brought to the airport by police, before making a series of “incoherent” demands.
Cyprus’ 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.”
Egyptian authorities said security measures had been “fully implemented” before the flight.
CCTV footage released by the interior ministry shows Seif Eldin Mustafa being frisked at two security checks and passing a slim bag through X-ray machines at Alexandria’s Borg El Arab airport.
Egypt has taken steps to improve airport security after Russian Metrojet Flight 9268 was blown up over Sinai in October 2015.
They include an extra $1 billion a year and a deal with British consultancy Control Risks to review procedures at Cairo, Sharm El-Sheikh and Marsa Alam airports.
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