High winds and unusually heavy rainfall have hit swathes of Austria, the Czech Republic, Hungary, Poland, Romania and Slovakia since Friday.
An 81-year-old woman is Austria's fifth victim of the floods, a police spokesman told AFP.
The fire brigade found the woman's body on Tuesday in her flooded home in Lower Austria, the worst-impacted province in the Alpine nation.
In addition to the five people killed in Austria, Storm Boris has caused the deaths of seven people in Romania, four in Poland, three in the Czech Republic, according to the latest tallies.
Although the weather seemed to be stabilising in several places, the ground remained saturated and rivers were overflowing, with authorities asking people to remain cautious.
In Austria, 26 communities were cut off and with the weather improving, "we are discovering the scale of the disaster", Lower Austrian governor Johanna Mikl-Leitner said.
In the Czech Republic, more than 60,000 homes were still without electricity, mainly in the country's northeast, and 500 people were evacuated on Monday evening, including children.
The largest Czech retention basin, the Rozmberk pond in the country's south, has been overflowing its banks.
Experts say climate change caused by greenhouse gas emissions generated by human activities is increasing the frequency and intensity of extreme weather events such as torrential rains and floods.
Andreas von Weissenberg of the International Federation of Red Cross and Red Crescent Societies (IFRC) said studies to determine whether climate change is linked to these events are expected in the coming months.
Von Weissenberg said local Red Cross teams were helping the rescue and evacuation efforts, including attending to people's "emotional and mental health".
He said the floods have been "branded as historic", but warned that "climate change has a way of moving the goalposts.