Floodwaters surged into a town in northern Austria yesterday as torrential rains disrupted rail services, cut a border crossing with Germany and sent emergency services on nationwide alert.

The river Inn burst its banks and part flooded the northern town of Schaerding, while the mighty Danube was rising to dangerous levels, a day after floods in central Europe left three people dead.

Water was rising at a rate of 70 centimetres per hour in the centre of Schaerding, firefighters said downriver, the border crossing was closed because of the flooding, which disrupted rail links across the Upper Austria region according to the state rail operator OBB.

Authorities were keeping close watch on the Danube, the country's biggest river, which has risen to 5.65 metres in the regional capital Linz. An emergency plan is to kick in if it passes the 6.20-metre mark.

Rescuers were also called out because of heavy rains across the regions of Salzburg in the north, Styria in the south and Vorarlberg and Tyrol in western Austria, with more rain forecast for today.

Authorites said Wednesday three people had been killed and hundreds evacuated after days of heavy rain in central Europe.

In the Czech Republic, two men drowned in swollen rivers and a 19-year-old man died when his car skidded on a flooded road, while in neighbouring Hungary about 2,000 people had to be evacuated from their homes after flooding.

Meanwhile, more than 90 per cent of farmland in eastern Croatia's agricultural regions were also under flood water yesterday and dozens of families were evacuated, local media reported.

Emergency services backed by military units were working to set up flood barriers along the banks of several local rivers, the reports said, as Nova TV said flood damage was of up to one billion kunas (€137 million).

About 100 families were evacuated from their homes in the region of Slavonski Brod and Vinkovci, it added.