Packets of cocaine were discovered in banana crates in seven Berlin supermarkets and in four shops in the surrounding state of Brandenburg on Thursday.
Supermarket workers found the packages lying under the fruit during the morning, police said. Tests later confirmed the packages were cocaine, but officers have not disclosed the quantity of cocaine involved.
The illegal drugs have now been confiscated from Lidl stores among others.
"Lidl is in dialogue with the relevant authorities regarding the incident," a Lidl spokeswoman said.
It is so far unclear why the cocaine ended up in the supermarkets rather than its intended target.
Germany's police union expressed little surprise at the discovery.
"Every now and then a delivery goes missing and ends up in the supermarket, especially as fruit crates are quite popular anyway for traffickers," the Berlin regional head of the police union, Stephan Weh, told dpa.
"We have been experiencing an absolute glut of cocaine for years."
Consignments of cocaine have repeatedly been found packed amongst bananas imported from South America in Germany and other European countries.
In September last year, German police found around 500 kilograms of cocaine in Groß Kreutz, west of Potsdam near Berlin.
A fruit and vegetable wholesaler informed police about suspicious-looking packages in boxes of bananas.
