The train carrying 70 passengers was heading from Athens to the second-biggest city of Thessaloniki when it derailed in the town of Adendro, some 37 km (23 miles) away, railway company TRAINOSE said. The cause of the accident was not yet known.
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 neighbour'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.
(Reporting by Karolina Tagaris; editing by David Clarke, Marguerita Choy and Dan Grebler)
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