Southern and eastern German cities are on high alert as heavy floodwaters swell rivers including the Elbe.
In Halle, an appeal has gone out to residents to help reinforce flood defenses while Dresden is preparing for water levels 5 m higher than normal.
German Chancellor Angela Merkel has promised 100 million euros ($130 million) in emergency aid for flood-hit areas.
Meanwhile, river levels in Prague have begun to fall, say the Czech authorities, as floodwaters move north.
Overnight, flood barriers on the River Vltava in the south of the country were raised, releasing a torrent of water.
However, Prague’s flood defenses appear to have held, and the risk of severe flooding in the city centre seems to be receding.
The city of Regensburg has declared a state of emergency, while in the state of Saxony – which includes Dresden – officials were warning of higher water levels than during the record floods of 2002.
The bodies of two people, a man and a woman, were found separately around the southern town of Guenzburg. At least seven people have died in the Czech Republic and two in Austria after days of heavy rain.
Hungary has also declared a state of emergency. Floodwaters on the Danube are expected to peak there on Thursday.
Germany has drafted in the army to help with flood defences.
In the Bavarian town of Passau, floodwaters reached a level not seen since the 16th Century, but have now begun to recede.
Chancellor Angela Merkel visited the worst affected regions on Tuesday, flying over Bavaria, Saxony and Thuringia by helicopter.
She promised 100 million euros in immediate aid, of which 50 million euros will go to Bavaria.
In the Czech Republic, a nationwide state of emergency is still in force. Water levels are expected to peak in the north later on Tuesday.
Around 3,000 people have been forced to leave their homes across the west of the country.
As a precaution, Prague’s metro system and central sewage treatment plant were closed, metal flood defenses were erected and sandbags built up along the banks of the Vltava.
The Charles Bridge – normally packed with tourists – was shut and tigers at the city’s zoo were tranquilized and moved out of an enclosure thought to be at risk.
A system of nine dams called the Vltava Cascade was found to be dangerously full, and the floodgates were opened at 20:00 local time on Monday night.
North of Prague, further downstream, the River Elbe is rising to levels approaching those seen in 2002, the last time Europe experienced similar floods.
Seventeen people were killed in the Czech Republic in August 2002 and the cost of the damage across the continent was estimated at 20 billion euros ($26 billion).
Main roads in many areas of central Europe have been closed and rail services cut. Thousands of homes are without power.
In Austria, the meteorological service said two months of rain had fallen in just two days.