Cities in southern and eastern Germany 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 defences while Dresden is preparing for water levels 5m higher than normal.
German Chancellor Angela Merkel has promised 100m euros (£78m; $130m) 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 defences appear to have held, and the risk of severe flooding in the city centre seems to be receding, says the BBC's correspondent there, Rob Cameron.
Water levels rise
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 100m euros in immediate aid, of which 50m 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 defences 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 tranquilised 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 (18:00 GMT) 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 20bn euros (£17bn).
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.
Floods across Central Europe
- Austria Two people have died and several are missing in the west of the country
- Germany Two people are dead and evacuations have taken place in Saxony, while more rain is forecast in Bavaria
- Czech Republic Seven people have died and Prague is on high alert. Troops have been called in to erect flood defences
One man was found dead near Salzburg and another in the western state of Vorarlberg. Three people remain missing.
More than 300 people were moved from their homes in Salzburg and the neighbouring Tyrol as the army worked with the civil authorities to clear landslides and make roads passable. Parts of the Pinzgau region have been declared a disaster zone.
In Germany, the army said it had sent 1,760 soldiers to southern and eastern areas to help local authorities reinforce flood defences.
Towns and cities in Saxony, Thuringia and Baden-Wuerttemberg have also been inundated.
Shipping was halted on parts of the Danube and Rhine rivers in Germany, and the entire length of the Danube in Austria. The rivers are used heavily to transport commodities such as grain and coal.
The European Union has said it stands ready to help the three countries as they tackle the devastating floods.
Slovakia's Prime Minister Robert Fico also warned that there was a risk of flooding as water moved down the Danube, which flows through Bratislava.
"We are getting bad news from Germany and Austria. We have to do all we can to protect... the capital," he said.
The head of Hungary's National Disaster Authority, Gyorgy Bakondi, said 400 people were working on flood defences in the capital, Budapest, where he said the level of the Danube might reach or even exceed the height seen in 2002.