The Cyprus Broadcasting Corporation said 55 people were on board on Tuesday, including seven crew. Sources said the plane was an Airbus 320.
At least one man was thought to be armed. The hijacking occurred in Cyprus's flight information region and the airliner was diverted to Larnaca.
Egyptian Plane with 55 People aboard Hijacked
Cyprus police said the hijacker contacted the control tower at 8:30 am (0530 GMT) and the plane was given permission to land at 8:50 am.
The man reportedly threatened the captain, saying he was wearing an explosive vest.
Egypt Air said the hijacker freed all on board except four foreigners and crew. He made no immediate demands.
The state news agency MENA said the hijacker is an Egyptian national called Ibrahim Samaha. He was sitting on seat K38, it said, without giving further details.
The Cyprus Broadcasting Corporation said the man has an ex-wife in Cyprus and may have personal motives.
Larnaca Airport has been closed and ambulances have been sent to the scene.
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