Raging waters from three rivers have flooded large parts of the south-east German town of Passau following days of heavy rainfall in central Europe.
A spokesman for the city's crisis centre said the situation was "extremely dramatic" and waters are expected to rise further by midday to their level highest in 70 years.
Much of the city is reportedly only accessible by boat and there are power outages in some areas.
At least four people have reportedly died and nine are missing due to floods in Germany, Austria, Switzerland and the Czech Republic in recent days.
Czech authorities have been scrambling to reinforce flood defences in Prague as the rising river Vltava threatened to engulf the capital's historic centre after days of heavy rain.
Prime Minister Petr Necas said 300 soldiers have been deployed to help local authorities and that up to 2,000 have been placed on standby.
The Czech government has declared a state of emergency in six regions that have been badly hit by the flooding, in the western half of the country and Prague.
Thousands of people have had to be relocated from their homes across the country, and a Prague hospital and zoo had to be partially evacuated.
Czech Prime Minister Petr Necas pledged 300 million Czech crowns ($15 million) to relief efforts and said another 2,000 troops were ready to support the 300 soldiers already helping to erect temporary barriers and pile sandbags in Prague and other areas.
"The government approved the declaration of a state of emergency, which will enable a more effective rescue effort," said Necas after an emergency cabinet meeting, adding that there was another 1.3 billion crowns available to help fund the cleanup operation.
The historic area of Prague is a UNESCO heritage site boasting hundreds of well-preserved buildings, churches and monuments dating back centuries, including the Charles Bridge straddling the Vltava that was closed due to high water
Czech Prime Minister Petr Necas declared a state of emergency for most of the nation on Sunday as swollen rivers caused by days of heavy rain threatened Prague's historic centre and forced evacuations from low-lying areas.
Prague authorities limited public transport and planned to close underground stations in the centre of the city as water from the Vltava River overflowed into picturesque areas popular with tourists
The main train line connecting the capital and the east of the country was also shut.