The robbery took place on February 9 at Deutsche Bank's headquarters in Frankfurt, but the bank only told the police this week, after internal investigations proved fruitless.
Bank spokesman Christian Streckert confirmed the robbery, but refused to add any further details.
Frankfurt police said the two water-colours, entitled "Swans" and painted in 1953, had an estimated value of €200,000. "Our investigations have so far had no results," a police spokesman said.
The Deutsche Bank's art collection was founded in the 1970s and now comprises over 56,000 works, mainly paintings and drawings, which are displayed all over the world.
Beuys, who died in 1986, is considered one of the most important German artists of the 20th century.