More than 23,000 people have been forced to leave their homes in the east German city of Magdeburg after a dam burst on the flood-swollen River Elbe.
Although water levels in Magdeburg were reported to be receding on Monday, the city and areas of the country further north remain on high alert.
In Hungary, 1,200 people had to leave their homes but flood defences in the capital Budapest appeared to have held, the BBC reported.
At least 18 people have died in the floods in Central Europe.
Parts of Poland’s capital Warsaw were flooded on Sunday after hours of heavy rain.
Hungary’s Prime Minister Viktor Orban said the capital “should be out of danger by Wednesday”, but warned that the focus of defence efforts was now in the south of the country.
A travel company offered customers a full refund after more than 120 passengers were stranded on a Danube river cruise due to torrential rain.