Czech rescue crews were searching for four others believed to have died in the flooding which cut power to tens of thousands of households across the Czech Republic, Austria and Germany.
The heavy rainfall has triggered nightmarish memories of devastating floods that killed dozens in the region in 2002.
In the Czech Republic, the government declared a state of emergency Sunday, deploying 2,000 troops in its rescue drive as five people died, several were missing and over 6,000 evacuated from their homes, officials said.
Two people died in a collapsed summer house south of Prague and three men drowned in rivers or drains in different parts of the country.
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The Czech capital was under water today, with metro stations and schools shut as the Vltava river rose, flooding parts of the historic city centre.
"You realise here what nature can do. How helpless we really are despite having all our technology," Prague pensioner Helena Holubova said, watching the water rise from a bridge over the Vltava in central Prague. The river was expected to peak in the capital later Monday.
Thousands of households were hit with power outages while fallen trees snarled rail traffic across western regions.
Heavy rain was expected to pelt the country until this afternoon, when forecasts called for it to taper off.
Flooding also deluged neighbouring Germany and Austria, killing at least one person there.
Two were reported missing and hundreds were also evacuated as landslides threatened their homes, mostly around the western Austrian city of Salzburg bordering Germany and in the north.
Memories of the 2002 flood also spooked residents in the nearby German city of Passau.
"A lot of people who already had to cope with major flooding in 2002 are refusing to leave their homes," Passau mayor Jurgen Duppen told Germany's N24 TV channel.