Two girls, aged four and eight, were killed when sudden strong winds toppled trees late on Thursday at a lake in the Lavant Valley of southern Austria.
Officials said 13 people were injured, two of them seriously. Many of the victims were holidaymakers visiting the tourist region.
Austrian president Alexander Van Der Bellen called the children's deaths "an unfathomable tragedy", while the mayor of the nearby town of Wolfsberg, Hannes Primus, said the area looked "like a battlefield".
In Lower Austria, three women were killed when lightning struck a tree near the central town of Gaming, causing it to fall over.
Fierce storms also killed at least seven people in France and Italy on Thursday.
French Interior Minister Gerald Darmanin said on Friday during a visit to Corsica that five people had been killed on the island.
Germany's national weather service DWD warned of "extremely abundant, prolonged rain" along the edge of the Alps that could see up to 140 litres of water per square metre fall over a 48-hour period that could cause flooding.
The Bavarian Red Cross said it was raising the alarm level for its air rescue specialists, putting helicopter crews on heightened alert.
