Eyewitness video shows violent winds and rain hitting Halkidiki, an area near Thessaloniki popular with holidaymakers, around 9.45 p.m. local time (2.45 p.m. ET).
An elderly Czech couple were killed when their caravan was blown over, and two Russians and two Romanians also died, according to CNN affiliate CNN Greece.
The localized storm reportedly only lasted around 10-15 minutes.
Other injured people were transferred to local hospitals and one was taken to intensive care, but all of them are in a stable condition, government spokesman Stelios Petsa was reported as saying by CNN Greece.
The local coastguard was also searching for a 62-year-old fisherman who went out to sea around 6 p.m. local time.
British tourist Kirstie Taylor, who filmed the video above, told CNN she was at Ikos resort in Halkidiki when the storm hit.
"It started with constant lightning, which went on for about 15 minutes. It was like someone switching a light on and off," she said.
"Then the storm happened very quickly. Chairs and tables were blown everywhere."
Family travel blogger Emily Kishtoo was at a beach party when the storm struck and the power cut out.
"There was screaming and people running about trying to get out of the beach bar and off the beach - there were probably around 200 people or so," she told CNN.
Kishtoo described grabbing her children and running back to her hotel in the torrential rain, with fallen trees and debris on the road.
"Things are still not back to normal here this morning, she said.
"The hotel is still on a generator, there is no running water, and the weather has turned cold."
Temperatures hit 37 degrees Celsius in the area on Monday, but dropped to 19 degrees Celsius early Thursday.
In September 2018 a rare hurricane-like storm triggered flooding as it hit southern Greece.
The storm, called Zorba, was dubbed a "Medicane" because of its location in the Mediterranean and its tropical-storm-like qualities.
Such storms only occur once or twice a year, usually during September and October, when sea surface temperatures are warm.
In early July large swathes of Europe were struck by a heatwave that pushed temperatures to record breaking levels.
The mercury reached 45.9 degrees Celsius (114.6 Fahrenheit) in Gallargues-le-Montueux in the Gard department in southern France, according to the French national weather service Météo-France.
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