Among commercial banks, hackers targeted Ceska sporitelna owned by Austria's Erste Bank, Komercni banka owned by France's Societe Generale, CSOB, which is in the hands of Belgium's KBC, and the local branch of Austria's Raiffeisenbank.
The banks insisted the so-called DDOS (distributed denial of service) attacks causing network overloads did not threaten client accounts or data.
The website of the Prague Stock Exchange was affected too.
On Monday, hackers attacked several top Czech news websites in the same way.
No information on the suspected culprits was immediately available. The website of the top-selling Czech broadsheet DNES said Monday's attack came from computers in Russia.
Last week, a wave of cyber attacks hit media and other sites worldwide, including Apple, Microsoft and Facebook.