OSE said the causes of the derailment were being investigated, and that "initial indications point to possible human error in traffic control".
A report from the Reuters news agency said the station master failed to change the points after a previous train had passed through, causing five carriages from the passenger train to jump the tracks.
On the run
The station master of the cargo-only station where the incident occurred is being sought by the authorities.
He has been missing since the incident occurred, Greek TV station Alpha reported.
The two drivers of the train were taken into custody for questioning, police said.
The accident came as tens of thousands of Greeks left the capital and other major cities for the countryside at the beginning of a three-day weekend. The coming Monday is a religious holiday.