Investigators sifting through the wreckage said that some of the bodies were frozen solid, suggesting some aboard were already dead before the Helios airlines plunged into the ground.
"Autopsy on passengers so far shows the bodies were frozen solid, including some whose skin was charred by flames from the crash," a Greek Defense Ministry source with access to the investigation told Reuters on Monday.
Later in the day a Greek coroner examining the victims said at least some of those on the flight were still alive at the time of the crash.
"Until now I have done an autopsy on six bodies and first evidence is that when they were killed they had circulation in their heart and lungs," Greek Chief Coroner Philippos Koutsaftis told reporters in Athens, according to Reuters.
"That does not mean that they were conscious but that they had breath and circulation. They had circulation and heartbeat so they were alive."
The state of the victims indicated to aviation experts that the Boeing 737 suffered a catastrophic loss of failure of cabin pressure or oxygen supply, but so far authorities have not been able to trace the source of the accident.
"Although there are precedents for both pilots losing consciousness at the controls of the aircraft in the past, for it to happen on a large airliner like a Boeing 737, with all the backup systems they have there, does seem to be really quite extraordinary," Kieran Daly, editor of Air Transport Intelligence, told The New York Times.
The jet was headed from Cyprus to Athens when it went down. All aboard, including some 17 children, died.
Authorities said they had already recovered the body of the pilot and the two flight recorders, the so-called "black boxes" that record pilot conversations as well as instrument readings. Although one of the recorders was said to be in "a very bad state," both boxes have already been sent to France for final examination.
Although authorities are still investigating what caused the crash, the Greek government acknowledged whatever occurred to the plane did not happen instantly.
Shortly before losing radio contact with Cypriot and Greek air traffic controllers, the pilots talked of problems with the jet's air conditioning system.
As the plane entered Greek airspace, the government in Athens dispatched fighter jets to intercept the 737 to find out what was wrong with the flight.
According to Greek government spokesman Theodore Roussopoulos, the F-16 pilots reported "a lifeless cockpit" and that the oxygen masks had deployed throughout the plane.
"The F-16s saw two individuals in the cockpit seemingly trying to regain control of the airplane," Roussoupoulos said, adding it was not known if they were passengers or other crew.
The jets stayed with the doomed Cypriot airline for more than an hour before the 737 crashed in a remote valley 25 miles north of Athens.
An earlier report concerning a text message from the flight before it crashed proved to be a fabrication. Police said they had arrested a man who said he had received a message reading, "The pilot has turned blue. Cousin farewell, we're freezing." The suspect has been charged with spreading false information.
The news of the crash sent grieving relatives streaming to the Larnaca airport from which the plane took off. Rumors of past problems with Helios aircraft prompted angry protests among the family members, some of whom shouted "murderers" at Helios officials.
Problems continued Monday, when more than 100 crew and passengers refused to board a Helios flight from Larnaca to Bulgaria.
"First the crew refused to board, then the passengers," the state-run Cyprus News Agency reported.
Helios also appeared to be under investigation in Cyprus, where police searched the airline's offices for what Cypriot Attorney General Petros Clerides told Reuters was "evidence that might be useful in a possible criminal investigation."