Frankfurt-based BaFin "ordered Deutsche Bank to take internal security measures and respect its general duty of care for the prevention of money laundering and terrorist financing," the agency said in a statement.
In January 2017, Deutsche had to pay a fine of almost $630 million (535 million euros) after an investigation by British and American authorities into laundering of money originating in Russia.
Soon afterward, the US Federal Reserve ordered a further fine of $41 million over gaps in the bank's money-laundering surveillance.
American lawmakers also demanded information about Deutsche's relationship with President Donald Trump and any financial links he might have with Russian entities.
Laundering of Russian cash has returned to the headlines in recent weeks, with Denmark's biggest lender Danske Bank admitting that tens of billions of euros of suspicious transactions passed through its branch in Estonia, most of them from Russia.
In neighboring Latvia, the central bank chief has also been suspended from his post after being charged with accepting bribes.
Malta, Estonia, Latvia, and Cyprus are among the countries with the worst money-laundering image in the 19-nation eurozone, although Spain's Caixabank and Netherlands-based ING have also come in for extra scrutiny by the authorities.