EgyptAir said negotiations had meant the majority of passengers have been released, but seven people -including three passengers, the captain, co-pilot, an air hostess and a security official remain onboard.
The civil aviation minister declined to give the nationalities of the passengers remaining on the hijacked plane.
Egyptian media earlier reported the hijacker to be university professor Ibrahim Samaha, aged in his forties, who is making political demands, while asking for a translator.
He was believed to be a professor of veterinary medicine at Alexandria University in Egypt.
However Samaha has spoken out to say he was in fact a passenger and has now been freed.
Local media reports also suggested the hijacker was making demands about his estranged wife.
Cypriot media said the professor threw a letter, written in Arabic, on to the tarmac of the airport after demanding it be sent to his ex-wife who lives in Lanarca.
She is reportedly being brought to the airport to negotiate with him.
The woman lives in the village of Oroklini, close to the airport.
Amid reports it is a “domestic dispute”, Cyprus President Nicos Anastasiades confirmed the Egypt plane hijacking was not related to “terrorism.”