The Süddeutsche newspaper said it had internal files from the Hypo-Vereinsbank (HVB) and the Swiss financial institute Sarasin showing how they were making a profit from tax statements.
Many other banks have been operating similar business models, the paper said, and said the financial authorities estimated that the total cost to the state was well over €10 billion.
A member of staff at the Munich-based HVB said that the scam involved doubling tax credits, exploiting a loophole in the law to get the tax authorities to refund capital gains tax twice.
It was clear within the bank that one was making money at the cost of the tax authorities, the source said.
The HVB has been conducting an internal investigation, the Süddeutsche said. It has admitted that it was taking part in such deals, alone and with business partners, between 2005 and 2008, amounting to around €200 million.