AFP reports the raid came shortly after Attorney-General Petros Clerides issued a warrant in the search for documents that could be useful in a possible future criminal investigation.
“We will investigate everything that is linked to the crash, those are the instructions from the government,” a police source told the local Antenna television station.
Aviation experts and investigators are struggling to unravel the cause of the crash described as Greece’s worst air tragedy.
Most of the victims were Cypriot and some 17 children are believed to have been among those who died.
Three Australians are also reported to be among the dead, a 39 year old man and his two daughters.
Officials said all but six of the 121 victims of the crash may have been dead before the plane smashed into a hill near Athens.
Relatives of victims have been arriving in Athens to identify the dead.
Flight 522 had been heading for Athens en-route to Prague when it lost contact with air traffic controllers.
That sparked a security alert before it crashed on Sunday afternoon but terrorism is not thought to be a factor.
Aviation experts believe a technical failure led either to a loss of cabin pressure or oxygen supply.
Coroner Philippos Koutsaftis told AFP that the main hypothesis for cause of death was asphyxiation.
However, a defence ministry source quoted by Reuters said it appeared that the bodies had been frozen solid.
Greek police have arrested a man who claimed his cousin sent him a farewell text message from the aircraft minutes before it crashed saying that everyone was frozen.
Relatives have accused Helios Airways of allowing an unsafe aircraft to take to the skies.
The Cypriot carrier denies the charge and has insisted that it is fully co-operating with investigators.
It has also denied a number of reports that it has grounded its entire fleet following the incident.