Flooding and heavy rains included Halkidiki, near the city of Thessaloniki, late Wednesday, officials said.
According to them, two Czechs, two Romanians and two Russians died.
Photographs and videos posted on social media showed trees falling, cars upside-down, and damaged buildings.
Authorities have declared the extraordinary situation while dispersing over 100 rescue experts.
Charalambos Steriadis, the head of the civil defense in North Greece, described the storm as an "unprecedented phenomenon".
The storm followed hot weather in Greece, with temperatures about 37 degrees Celsius over the past two days.