Some 23,000 people were 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.
At least 18 people have died in the floods in Central Europe.
Analysts say the damage will cost billions of euros to clean up.
Meanwhile, parts of Poland's capital Warsaw were flooded on Sunday after hours of heavy rain.
One of the city's busiest motorways was inundated, and firefighters had to help stranded drivers to safety.
Flood defences in Budapest appeared to have held on Monday as waters from the Danube River started to recede, having reached an historic peak of 8.91m (29 ft) on Sunday.
"We have no reports of any catastrophic situation, the situation is normalising," Budapest Mayor Istvan Tarlos said on Monday.
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.
More than 1,200 people have been evacuated from their homes, although no flood-related deaths have yet been reported in Hungary.Along more than 700km (470 miles) of the River Danube, thousands of people, including many volunteers and even convicts from the prisons, worked to reinforce earth and sandbag barriers.
In Magdeburg, the capital of Saxony-Anhalt state, flood waters rose to 7.44m (24ft), nearly four times higher than normal (2m) - forcing some 10% of the population, 23,000, to leave their homes.
Around 700 soldiers worked to build a dam of sandbags around a power sub-station in the badly-hit area of Rothensee in a bid to keep the power on.
The Suddeutsche Zeitung newspaper reported that flood water levels had fallen slightly in Magdeburg itself on Monday, but the situation remains critical.
"We hope that the dykes will withstand the pressure over the coming days, but we can't be 100% sure," said a fire brigade spokesman, Andreas Hamann.
But other parts of Saxony-Anhalt and neighbouring Brandenburg state remain under threat as the flood crest moves north, testing flood defences already weakened by days of heavy rain.
A dyke at Fischbeck, west of Berlin, was reported to have breached overnight, forcing the closure of a major train line linking Berlin to Cologne, Frankfurt and Amsterdam.
The authorities in Germany are investigating an anonymous letter threatening attacks on several dams.
The motive behind the threats is not known, but the threat is being taken seriously, says the BBC's Stephen Evans in Berlin.
Chancellor Angela Merkel is planning a crisis meeting with leaders of Germany's regions on how to share the bill for the disaster, the Leipziger Volkszeitung newspaper reported.
"We're dealing with a national catastrophe," Gerda Hasselfeldt, an MP with Mrs Merkel's Christian Social Union (CSU), was quoted as saying.