EgyptAir MS804 from Paris to Cairo disappeared from radar screens between the Greek island of Crete and the north coast of Egypt on May 19.
Investigators are still searching for the Airbus A320's two black boxes on the seabed as they seek answers as to why the aircraft went down.
Clutching bouquets of flowers, candles and the Egyptian flag, around 500 mourners assembled at the Cairo Opera House and observed a minute's silence in honour of the victims.
"We are here to pay respect to the souls of our victims and wish their families peace," said Civil Aviation Minister Sherif Fathy.
A large panel bearing the names of the 66 victims was displayed at the memorial ceremony, which was also attended by cabin crew in EgyptAir uniforms.
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"This is a message to the world that Egypt is a country of security and confidence and that people should not be afraid to come," said Jihan Halawa, one of the mourners.
Among those aboard MS804 were 30 Egyptians, 15 French citizens, two Iraqis, two Canadians, and citizens from Algeria, Belgium, Britain, Chad, Portugal, Saudi Arabia and Sudan.
They also included a boy and two babies, and seven crew and three security personnel.
Egypt and France will hire two private firms to help the hunt for the black boxes, the French foreign ministry said Thursday.
Aviation officials from the two countries have said it is too soon to determine what caused the disaster although a terror attack on the plane has not been ruled out.
They will share the costs for the search, which faces a race against the clock, as the flight data and voice recorders emit locator "pings" for no more than about a month.