Many roads were closed, particularly in the west and north of the country, and several rail services were disrupted after days of pelting rain that has left many parts of the country under flood alert.
Hundreds of fire fighters and emergency services, as well as the Austrian army, have been mobilised to help clear roads, assist with evacuations and put up anti-flood barriers.
Open-air music festivals and other events have also been relocated or partly cancelled as a result of the weather.
In Taxenbach near Salzburg, rescue services were still searching for two people believed to have been caught in a landslide - a farmer on a tractor and a woman in a car.
One woman is known to have died and three rescue workers are missing after the southern part of the Czech Republic was hit by flash floods.
Forty southern cities and towns are on maximum disaster alert. The authorities in Prague have issued evacuation orders.
In Germany, the Danube and the upper Elbe have burst their banks. In Baden-Wurttemberg, two persons are missing. In Passau, Bavaria, the Danube is flowing at 9.3 meters above its normal level. A number of central streets are covered with water.
The highest level of danger was announced in 19 Czech communities this morning.
The situation was aggravated by heavy rains in the country’s southern regions on Saturday night.
Steady rains caused floods in Germany. The town of Stadtroda has been partially flooded. The water level in the area of the town of Passau has passed the 7.5m mark.
In some regions of Switzerland the situation also gives reasons for concern. In particular, preparations for a flood are taking place around Lucerne. Navigation has been stopped on the Rheine near Basel.
Meteorologists are still in no position to say when the situation would go back to normal.