Hundreds of people were trapped in flooded buildings as Cyclone Ianos, known as a "medicane" (Mediterranean hurricane), battered areas north of Athens.
Prime Minister Kyriakos Mitsotakis has sent three senior officials to the worst-hit central region.
Train services linking the north and south of the country have been cut.
Footage on social media showed huge waves lashing the beaches on the Ionian islands of Kefalonia and Zakynthos on Friday as the storm headed in. Flights and ferry services were cancelled and tourists were advised to stay indoors.
As Ianos churned eastwards overnight, the city of Karditsa north of Athens was lashed by winds of up to 120km/h (75mph) that brought down trees and power lines and triggered landslides.