Egyptian Seif al-Din Mohamed Mostafa is accused of using a fake suicide belt to force the Alexandria-to-Cairo flight to divert to Cyprus on Tuesday, and has been remanded into custody in Cyprus.
He said he acted out of desperation to see his ex-wife and children who live in the eastern Mediterranean island.
"Immediately after the hijacking, I asked the security officer to stay at the door of the cockpit and not leave," EgyptAir pilot Amr Al-Gamal told reporters in a meeting organised by Egyptian authorities.
Systems that lock a cockpit door have existed since the 1980s and strict procedures became standard after the September 11, 2001 terror attacks.
"Our main fear was that the hijacker may enter the cockpit, or that he knew how to fly a plane or use it to explode", said co-pilot Hamad al-Qaddah.
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Mostafa released most of the 55 passengers soon after the plane landed in Larnaca, Cyprus. Hours later he surrendered to police.
Cypriot police say Mostafa -- described by officials as "psychologically unstable" -- faces possible charges of hijacking, kidnapping, reckless and threatening behaviour, and breaches of the anti-terror law.
For the crew it was an six-hour long emotional drama that saw a British passenger taking a photograph with Mostafa and a co-pilot escaping by jumping out of a window of the cockpit.
"The captain asked us to take a photo of the hijacker," said stewardess Nayera Atef al-Dabs, whose photograph with Mostafa wearing what appears to be a rudimentary suicide vest strapped to his chest has gone viral on the Internet.
She said she posed for a picture with Mostafa after a British passenger did the same.
"I was crying in the bathroom and I called my sister to tell her to take care of my three-year-old son. I was trying to look calm in front of the passengers," said Dabs, recalling Tuesday's ordeal.