At least 17 people died in flash floods in the Macedonian capital Skopje during a storm yesterday, Deputy Prime Minister Nikola Todorov said.
He also warned that the death toll could rise further.
Torrential rains had swept away a section of the ring road around Skopje and some cars had been carried hundreds of metres away into nearby fields, it was reported.
"This is a catastrophe of unprecedented proportion," Mr Todorov said. He said he had received unconfirmed reports of three further deaths.
Northern suburbs of Skopje were particularly hard hit, with many homes flooded. There were also flash floods in the city centre.
Special police forces and trucks loaded with drinking water were heading for the worst affected areas and there were some electricity outages.
The rain had stopped this morning and water levels were receding, but more rain was forecast for this evening in the capital of the small Balkan nation of two million inhabitants.
European Union Enlargement Commissioner Johannes Hahn said on Twitter that the EU stood ready to help Macedonia, which is a candidate to join the bloc.
Further north in the Balkans, in Croatia, heavy winds caused disruptions on some roads, including the closure of the highway linking the capital Zagreb to the southern coast, local media said.
Violent storms also battered the northwestern city of Tetovo causing property damage but no casualties, while severe thunderstorms also affected the holiday spot of Lake Ohrid in the southwest.
Skopje previously suffered disastrous flooding in 1962, a year before a huge earthquake that almost destroyed the city.
In the spring of 2014, the Balkans region was hit by its worst floods in more than a century, which left 47 people dead in Serbia and Bosnia.