Greek emergency services on Thursday were trying to rescue potentially dozens of people from villages in a central region that has seen more rain in 24 hours than it normally sees in a year.
Fierce storms battered Greece, Turkey and Bulgaria earlier this week, following a period of extreme heat and devastating wildfires.
A "large-scale" operation was underway to reach villages near the town of Karditsa, where the water level had risen between 1.5 and two metres (five-seven feet), fire service spokesman Yannis Artopios told public TV broadcaster Ert.
"It's very difficult to reach them," he added.
The mayor of the Palamas district, where Karditsa is located, told private TV channel Skai that villagers were stuck in their homes "without any form of assistance".
The channel showed footage of houses underwater.
At least 14 people have been killed by the downpours in Greece, Turkey and Bulgaria countries.
Such extreme weather is becoming more frequent and more intense as a result of human-induced climate change.
Interior Minister Niki Kerameus said the authorities were starting to evaluate the damage from the storm and floods.
Local residents, farmers and businesses would be compensated, he told Skai on Thursday.
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