The investigation was in connection with the Duesseldorf-based Defense Industries Organization (DIO), a company that is suspected of illegal arms deals with Iran, the Cologne/Bonn Rundschau newspaper reported. In a report to appear in its Saturday editions, the paper said the money for the alleged deals was believed to have been handled by the two banks.
The paper quoted Duesseldorf prosecutor Peter Lichtenberg as confirming that the searches took place on Thursday.
No one answered the phones at the prosecutor's offices or the banks late Friday.
Prosecutors ordered a search of DIO late last year and said they had confiscated files and other material.