The canton of Lucerne was the worst hit by hail with car owners reporting damage mounting into several million francs, the ATS news agency reported.
Areas around the cantons of Zug and Zurich were also hard hit, the agency said.
Insurer Allianz Suisse registered 200 calls from people claiming five million francs in damage, the company said.
It expects to deal with a total of 2,000 cases of hail damage when all claims are received.
Farmers also suffered extensive crop damage from the hail, according to the Suisse Grêle hail insurance cooperative.
The coop told ATS it expects to receive 200 claims for damage estimated at 500,000 francs.
The storm brought heavy rain to areas around Lake Geneva, the Vaud Alps, Fribourg and Bern, causing flooding in some communities.
Villages in the Lavaux wine region, east of Lausanne in the canton of Vaud, were particularly hard hit.
Water flooded streets in Cully, Grandvaux and Riex, according to media reports while the intense rain brought traffic on the A-9 motorway east of Lausanne to a crawl.
MeteoSwiss, the national weather office, is forecasting the possibility of further stormy weather in German-speaking Switzerland ion Friday afternoon.