One carriage crashed into the ground floor of a two-storey house while others toppled onto their sides, their windows smashed.
The driver was in critical condition, TRAINOSE said.
The fire brigade and the head of the National Emergency Service said two people were killed. Earlier, in a statement on its website, TRAINOSE had said four people died in the crash. It later removed that reference.
"Death came calling," the Athens News Agency quoted Yorgos Mylonas, a local resident, as saying. "I heard a strange noise and then I saw the train approaching and ramming into my neighbor's house," he said.
Some media said five carriages had derailed.
At least 12 fire trucks were deployed to the area, the fire brigade said, in a rescue operation which lasted into the night.
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00:37
At least 10 people were injured when a passenger train derailed in northern Greece on Saturday night, fire brigade and police officials said.
Photographs on Greek news websites showed one carriage on its side near a residential area.
The train was heading from Athens to the second biggest city Thessaloniki in northern Greece when it derailed near the town of Adendro. Its engine was propelled into a nearby house but the cause of the accident was not yet known, a police official said.
The Athens News Agency reported about 100 passengers were on board the train and some media said five carriages had derailed.
Twelve fire brigade trucks were deployed to the area, the fire brigade said and a rescue operation was under way.
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