In what has been described as Greece’s worst air disaster, the jet hit a hill near Athens after both pilots apparently fell unconscious after a drop in cabin pressure.
Contact with the Helios Airways plane was lost during the flight between Larnaca in Cyprus and Athens.
Two Greek F-16 fighter jets were dispatched to investigate.
Government officials said the fighter pilots saw two people in the cockpit.
“We didn’t know if they were crew members or passengers appearing to want to take over the controls,” said government spokesman, Theodore Roussopoulos.
He added that they saw “the co-pilot slumped over and perhaps unconscious and the pilot not in his seat.”
Greek television reported a harrowing account from a passenger who apparently sent a text message to a cousin which said “We’re cold. The pilot is blue. We’re going to die. Farewell.”
The pilots had reportedly had problems with the plane’s air conditioning before losing radio contact.
Officials say there is no reason to suspect terrorism and the indications so far show that the crash was an accident.
One of the plane’s two black boxes containing the flight data recorder has been recovered.
US investigators are on their way to Athens to assist the inquiry.
An expert said the investigation is likely to focus on whether a sudden depressurisation in the cockpit overcame the pilots before they could take on oxygen and bring the aircraft to a lower, safer altitude.
But a French investigator has told AFP that a sudden loss of pressurisation would not have caused the plane to crash, nor would it have made the pilots immediately lose consciousness.
An airline official said most of the passengers were Cypriot.
They included around 48 children on a trip to Prague, where the plane was due to fly after a stopover in Athens.
“There were also a certain number of Greeks and only a few foreigners,” said the official, George Dimitriou.
A Greek fire chief said there were no survivors.
Greece has declared a day of mourning for Tuesday when flags will fly at half-mast and a three-minute silence will be observed in public buildings.