Police told the court in Larnaca that 58-year-old Egyptian Seif al-Din Mohamed Mostafa faces possible charges of hijacking, kidnapping people with the aim of taking them to an unknown destination, reckless and threatening behaviour and offences that breach the anti-terror law.
The accused did not speak in court.
But as he left in a police car, he gave the victory sign to journalists attending the hearing at the courthouse, which is less than a kilometre (half a mile) away from Larnaca airport where the hijacking unfolded on Tuesday.
Cyprus authorities have described Mostafa as "psychologically unstable" and said the case was not "terrorism-related".
He is accused of forcing the plane to divert to Larnaca airport on the island's south coast on Tuesday by threatening to detonate an explosives belt that turned out to be fake.
Authorities allege that his motives were personal and related to his Cypriot ex-wife with whom he is reported to have had children.
The hijacking triggered a six-hour standoff at the airport and the closure of the main entry point for tourists to the Mediterranean resort island.
But some escaped only minutes before the standoff ended, including one uniformed man who was seen clambering out of a cockpit window and dropping to the ground.
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