Ratings agency Moody's has cut the credit ratings of six German banks and three in Austria.
The biggest bank affected was Commerzbank, Germany's second-biggest lender, which was cut to A3 from A2.
Moody's delayed a decision on the rating of Germany's biggest bank, Deutsche Bank.
"Today's rating actions are driven by the increased risk of further shocks emanating from the euro area debt crisis," Moody's said.
The downgrade indicates that Moody's thinks Germany would be hit if the euro crisis turned into a catastrophe, said BBC Berlin correspondent Stephen Evans.
"It brings the crisis in Southern Europe and Ireland closer to home in Germany," he said.
The six German banking groups affected were Commerzbank, DekaBank, DZ Bank, Landesbank Baden-Wuerttemberg, Landesbank Hessen-Thueringen and Norddeutsche Landesbank.
Moody's also cut the rating of the Italian bank UniCredit's German unit.
In Austria, it downgraded the three biggest banks: Erste Group Bank, UniCredit Bank Austria and Raiffeisen Bank International.
The ratings agency said Austrian banks were also vulnerable to conditions in central and eastern Europe as well as the Commonwealth of Independent States.
It also said that banks in Germany and Austria had a limited capacity to absorb losses.
In addition to having its rating cut, Commerzbank was placed on negative outlook, meaning Moody's is considering a further cut. The agency said that was because of the bank's exposure to the eurozone periphery, as well as its concentration of loans to single sectors and borrowers.
Another German bank, WGZ Bank, was not downgraded, but was placed on negative outlook as a result of its exposure to the debt of the eurozone's periphery.
The downgrades came as the focus remained on banks in weaker eurozone economies, amid fears that those in Cyprus and Spain could need more support.
The European Commission is due to announce plans later to make sure that failed banks do not have to be bailed out by taxpayers in future.