Nineteen convicts escaped from prison in Bosnia last night while their guards manned defences against the worst floods to hit the Balkans in living memory.

"There was confusion inside the prison," local police duty officer Pavo Grgic told Reuters on Wednesday. "The prisoners were panicking as the water in their cells was already one metre deep. They took the opportunity when the building was lightly guarded and fled."

Six prisoners were arrested shortly after the escape in the northern Bosnian town of Orasje while the rest were apprehended in the morning after a night-long manhunt.

Grgic said all prisoners had since been relocated to prisons in the central town of Zenica and northern Tuzla. He declined to give any further details of the jailbreak.

At least 40 people have died in Bosnia, Serbia and Croatia after the heaviest rainfall since records began 120 years ago caused rivers to burst their banks and triggered hundreds of landslides.