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.
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.
The floods have killed at least two people and left several missing across the Czech Republic, and also prompted officials to evacuate a Prague hospital and parts of the zoo.
Rising rivers have forced the closures of highways and railway lines throughout western and southern Bohemia. Utility companies reported outages throughout the region after floods damaged a number of substations.
"The water is about 50 metres from my house but it's only 1 or 2 metres from other houses," said Rory Pattison, an expatriate worker living in a village just outside Prague.
"We haven't had an evacuation notice yet but everyone is making preparations just in case."
The situation brought back memories of floods in 2002 that killed 17 people, forced tens of thousands from their homes and caused several billion dollars of damage across the country.
Water levels have not reached that point yet but weather forecasters predict the rain will continue for at least another few days, raising the prospect that rivers have not yet peaked.
Following the disaster in 2002, the Czech government spent $150 million on installing an anti-flood system to protect Prague, a city which generates much-needed tourism revenue for state coffers.