Rescuers were concentrating their efforts on Monday on locating the bodies of the two remaining victims in the burned wreckage of the aircraft at the bottom of a ravine, an AFP photographer at the scene reported.
The search for bodies from Sunday's crash had gone on throughout the night under powerful arc lights.
The Interior Ministry said identifiable bodies would be taken to an establishment at Goudi, near Athens city centre, where relatives could begin identifying them.
Remains that were not identifiable would be DNA tested at the mortuary in the port of Pireus, where all the bodies had been taken initially, Interior Minister Prokopiis Pavlopoulos said after a meeting during the night with Cypriot officials.
Black flight boxes
Relatives of the victims were expected to arrive in Greece early on Monday on a chartered flight.
The head of the investigation into the crash, Akrivos Tsolakis, confirmed the discovery of the plane's second "black box", containing recordings of the pilots' cockpit conversations, but said it was in a "very bad state".
Relatives of victims are to arrive
in Greece to identify bodies
"We don't know if we will be able to get something from it," he said.
That and the other black flight box, the flight data recorder, would be sent to Paris for analysis, under agreement between France and Greece, Tsolakis said.
Dead before crash
Greek Interior Minister Prokopis Pavlopoulos said on Monday that most or all of the 121 passengers and crew on the airliner were probably dead before the plane hit the ground.
"It seems that death in many if not all cases happened before the crash, but that is something which we will have to confirm," the minister said in a statement.
Investigators continue to search
"I stress that with reservation because we are studying all possibilities," he said.
The minister did not say what caused the deaths, but the Greek national television Net said autopsies would establish whether the victims died of asphyxiation because of a lack of oxygen in the aircraft cabin.
On Sunday night, Greek government spokesman Theodoros Roussopoulos indicated that the pilot had reported problems with the Boeing 737's air-conditioning system in his last message to air traffic control.
Two air force F-16s that scrambled to escort the plane after contact was lost saw the co-pilot slumped over in the cockpit, possibly unconscious, while the captain was not in his seat and the oxygen masks were down.
"It seems that death in many if not all cases happened before the crash, but that is something which we will have to confirm"
Greek interior minister
The Helios Airways Boeing 737 was about to land at Athens airport for a stopover on its journey from Larnaca in Cyprus to the Czech capital, Prague, when it crashed at Varnava, a largely uninhabited area 40km northeast of Athens.
Helios said most of the passengers were Cypriots, including a group of 48 youngsters on their way to Prague.
The cause of the crash remains unknown.