A driver trying to avoid debris in the northern region of Halkidiki fell into a ditch Sunday and died of hypothermia in his vehicle, state broadcaster ERT said.
Storm Bora, which arrived in Greece on Saturday, is forecast to bring heavy snowfall to the north and northwest until Tuesday.
More than 17 centimetres (6.7 inches) of rain fell in 12 hours on Saturday, the Greek weather service said.
Hundreds of homes have been flooded and several areas have been hit with power cuts.
"Storm Bora constitutes additional proof that what we knew about natural phenomena is no longer valid," government spokesman Pavlos Marinakis told reporters Monday.
"We call on all citizens to follow authorities' instructions until the phenomenon abates," he said.
Two men died on Lemnos in the Aegean sea on Saturday after the civil protection service issued an emergency alert for torrential rains and strong winds in the northeast, the centre and the region around Athens.
One 57-year-old man died while trying to pull his car out of the mud with a tractor, while a 70-year-old fell on his head outside his home.
Floods filled many fields on the island, whose economy relies on farming.
On the island of Rhodes, which has an important tourist industry, the storm damaged roads, houses and commercial buildings overnight on Saturday to Sunday, regional governor George Hadjimarkos said.
He said scores of people had been evacuated. One bridge was swept away while cars were piled on top of each other after being carried by torrents.
The storm also knocked out rail services in central Greece after flooding tunnels in Tempi, site of the 2023 train collision that claimed 57 lives.
