In the Czech Republic, where the deaths of at least seven people were attributed to floodwaters and 3,000 people were forced from their homes, dams were opened to relieve the pressure, pushing the River Vltava higher. The river, which flows through Prague, the capital, was expected to crest Tuesday morning, the BBC reported.
Two more people were killed in Austria, the British network said.
In Germany, soldiers were deployed to beef up flood barriers. The people of Passau -- known as the "City of Three Rivers" because the Danube, Inn and Ilz converge there -- witnessed floodwaters not seen since the 16th century, the BBC said. Much of the city of 50,000 was inaccessible and a state of emergency was declared.
The BBC said the body of a man swept away while clearing a landslide was found near Salzburg, Austria, where more than 300 people fled their homes because of flooding, and another man was found dead in the state of Vorarlberg, the BBC said.
Main roads throughout central Europe were closed and rail service was cut. Electricity in some areas was turned off as a precaution.
At least eight people were reported missing, including three in Austria, officials said.
In Germany, more than 7,000 people were evacuated from their homes in Eilenburg. The city of Rosenheim also was under a state of emergency.
In Saxony, water levels on the River Mulde were said to be particularly high.
Bavaria's flood-alert service said the forecast called for heavy rain that could worsen the flooding along the Danube and the Inn rivers, and other rivers in the area.
Prague was on high alert amid fears floodwaters could envelope its historic center, including the 14th century Charles Bridge and other buildings near the riverbank.
More than 2,500 people were forced to flee in the capital and its surrounding area, Radio Prague reported.
Underground train stations and schools were closed while officials waited to see if the Vltava River would overflow its banks.
"We will do everything to protect people's lives and health," Czech Prime Minister Petr Necas said. "Tonight and tomorrow will be critical."
Necas called a special Cabinet session Sunday to coordinate an emergency response and mobilized 1,000 troops to help erect metal barriers and fill sandbags.
Acting Prague Mayor Tomas Hudecek told CTK vehicular and public transit would be restricted indefinitely and called on people not to go to Prague unless it was necessary.
In Austria, the meteorological service said two months of rain fell in just two days, the BBC said.
More than 300 people were evacuated in Salzburg and Tyrol, and the Austrian army worked with civil authorities to clear landslides and roads.
Parts of the Pinzgau region were declared a disaster zone.