Eifel Zoo has nearly 400 animals of 60 exotic and native species, including lions, tigers, and other big cats on its 30-acre site. Area residents were advised to stay in their houses, close their doors and windows and keep an eye out for the missing animals.
Most were found on the grounds of the zoo and returned to their cages.
Heavy rainstorms overnight had sparked flash floods.
According to the German broadcaster, heavy rain meant the water level increased and nearly the "entire zoo was flooded".
Petrol, Diesel Prices Rise For 16th Day
The rises are blamed on an increase in oil prices to above $80 (£60) a barrel, combined with a poor exchange rate for the pound. Petrol and diesel prices today were hiked for the sixteenth straight day across the country.
Part of a local motorway had been blocked off due to high waters, and a train was derailed although no injuries were reported.
This June 2016 image shows lion Malor (behind) and the mother Lira in their enclosure in the Eifel Zoo, eastern Germany.
The zoo opened in 1965 with dogs, donkeys and a wild boar, but has since expanded and is now home to 400 animals of 60 species, including Siberian tigers and lions, and sees around 70,000 people visit per year. One was captured, the other shot dead.
Authorities said a river running through the zoo complex had burst its banks, allowing the five cats and a bear to swim out of their enclosures.