The Cyprus Broadcasting Corporation reported that 55 people were on board, with a crew of 7. There were earlier reports of about 80 to 81 people on board.
The hijackers contacted the control tower at 8:30 am (0530 GMT) and the plane was given permission to land at 8:50 am, the police said.
EgyptAir confirmed the hijacking on Twitter.
The hijackers made no immediate demands and a crisis team has been deployed to the airportOur flight MS181 is officially hijacked. we'll publish an official statement now. #Egyptair- EGYPTAIR (@EGYPTAIR) Tuesday March 29,2016
The EgyptAir plane was flying from the Egyptian coastal city of Alexandria to the capital, Cairo.
The hijacker, identified as Seif Eldin Mustafa, is seen wearing his 'suicide belt',hijacked the domestic EgyptAir jet after taking off from Alexandria and forcing it to re-route to Cyprus' Larnaca airport, where he has taken several passengers and crew hostage and demanded to see his Cypriot ex-wife.
Cyprus airport hostage drama ends, EgyptAir hijacker surrenders
The hijacking of an EgyptAir flight that was diverted to Cyprus ended on Tuesday with all hostages being released and the hijacker surrendering.
A man believed to be the hijacker of the EgyptAir Airbus A-320, leaves the plane before surrendering to security forces at Larnaca airport.
The hijacker emerged from the aircraft with his hands in the air nearly six hours after he took over the plane, Cyprus's state broadcaster said. "It's over. The hijacker arrested," the Cypriot foreign ministry said.
Cyprus' foreign ministry identified the hijacker as Seif Eldin Mustafa. He was taken into custody after he released all the passengers and crew.
His surrender ended an hours-long drama and standoff at the Larnaca airport in southern Cyprus. The hijacker had earlier freed most of the passengers but kept seven people - four crew members and three passengers - with him.
Just minutes before the arrest, local TV footage from the airport showed several people disembarking from the aircraft and a man who appeared to be a crew member climbing out of the cockpit window and sliding down the side of the plane.