Throughout hilly Bosnia, floods are triggering landslides covering roads, homes and whole villages. About 300 landslides have been reported, and stranded villagers often are being rescued by helicopter.
"The situation is catastrophic," said Bosnia's refugee minister, Adil Osmanovic.
Three months' worth of rain fell on the region in a three-day burst, creating the worst floods since rainfall measurements began 120 years ago.
While water levels are receding in some parts of Bosnia, land flanking the Sava River remains submerged. Hundreds of people have been plucked by rescue helicopters from flooded towns and villages.
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An estimated 10,000 people have been forced from their homes in flooded villages around the eastern town of Bijeljina, where the Sava River broke through defences yesterday.
The overflowing river rolled over villages and farm land in the relatively flat terrain.
In Serbia, more than 20,000 people have been forced from their homes. Officials there fear more flooding later today as floodwaters travel down the Sava and reach the country.
Serbian officials said that the flood wave might be lower than initially expected, because the river broke barriers upstream in Croatia and Bosnia. Experts said they expect Sava floodwaters to rise for two more days, then subside.