"We cannot rule anything out," Ismail told reporters at Cairo airport.
Airline officials and the Egyptian Civil Aviation Department said they believed the plane had crashed in the Mediterranean between Greece and Egypt.
In Athens, Greek Defense Minister Panos Kammenos said the plane made sudden swerves in midair before disappearing.
Greece deployed aircraft and a frigate to the area to help with the search.
A Greek Defense Ministry source said authorities were also investigating an account from the captain of a merchant ship who reported a "flame in the sky" about 130 nautical miles south of the island of Karpathos.
According to Greece's civil aviation chief, attempts by Greek air traffic controllers to contact the jet went unanswered just before it left the country's airspace, and the plane disappeared from radar screens soon afterward.
The aircraft was carrying 56 passengers — including one child and two infants — and a crew of 10, EgyptAir said. Among them were 30 Egyptian and 15 French nationals and citizens of 10 other countries.
With its archaeological sites and Red Sea resorts, Egypt is traditionally a popular destination for Western tourists. But the industry has been badly hit by the downing of a Russian Metrojet flight in October, killing all 224 on board, an Islamist insurgency and a string of bomb attacks.