Authorities on the Greek island of Evia said several areas were being evacuated following the second severe storm in under a week.
Hundreds of homes in the Greek capital Athens, with some residents in remote areas airlifted to safety by rescue helicopter.
Dozens of vehicles were stranded on flooded roads, forcing the people inside to abandon their vehicles and wade through the water to safety.
“There is no doubt that we are facing a dangerous weather phenomenon that is very serious in some parts of the country,” said Civil Protection and Climate Change Minister Christos Stylianides.
Northern Evia, about 130 kilometres northeast of Athens, suffered devastating fires over the summer, leaving the area more vulnerable to flash floods.
Dozens of residents were moved out of their homes in the north of the island and were making arrangements to stay with friends or at hotel rooms booked by the regional authority.
Thursday’s storms battered Athens and other parts of southern Greece, causing traffic disruptions and some road closures.
The fire service received more than 300 calls in the capital to pump water out of flooded homes, authorities said.
The government issued alerts to the affected areas, urging people to "avoid unnecessary movement and areas that have been or may be flooded".
The weather in the country is expected to improve by Saturday.