Agriculture Minister Ilse Aigner said the judiciary must "clamp down hard".
Germany has frozen sales from thousands of farms after high levels of dioxin - which can cause cancer - were found in animal feed and eggs.
The contamination stems from a plant in Northern Germany, which is being investigated by prosecutors.
"This is a big blow for our farmers. They have totally innocently been dragged into this situation by the sick machinations of a few people," Ms Aigner told the Bild am Sonntag newspaper.
"It is tough enough to shake off the suspicion, given what we know so far, that criminal energy was combined with an alarming unscrupulousness."
Some 4,700 German farms were banned from making deliveries after tests at the Harles und Jentzsch plant in the state of Schleswig-Holstein, which produces fats for use in industrial processes as well as to enrich animal feed. But 3,000 have since been given the all-clear.
The Republic of Korea and Slovakia reacted by blocking imports of German meat and poultry products, although the European Commission said on Saturday there were no grounds for such a ban.
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