"Rat poison should not be put anywhere near food," said Armin Valet from the Central Consumer Association. "That is in our opinion a breach because it presents a threat to health."
Public broadcaster ARD said the chain had not told customers about the poison used in the retail areas of branches in the states of Lower Saxony, Bavaria and Berlin.
The ARD show Kontraste said a lab found "significant toxicity" in samples taken from one supermarket in Berlin.
One employee told the show the chain was using "pink poison" that wasn't particularly dangerous for humans. But a blue pesticide could cause "serious burns" and even "heart failure," she said, adding that customers had not been informed of the danger.
Lidl said it was taking the claims seriously, and that it put customer safety first. "It is possible to shop at Lidl safely," said a spokesman.