More than 200,000 ducks would be slaughtered at two farms in Bavaria to avoid bird flu spreading.
The head of Bavaria's state office for health and food safety, Volker Hingst, said the slaughter was "a purely precautionary measure," taken after "laboratory indications of H5N1" were found. The birds were not visibly sick, he said.
The two farms are located near Schwandorf, east of Nuremberg, and have a total of 205,000 ducks. It was not immediately clear how the virus might have gotten there.
Last month, more than 160,000 ducks were slaughtered at another Bavarian poultry farm following an outbreak of the disease. Officials have said that contaminated straw was the likely source in that case.
The two businesses affected Friday are subsidiaries of that farm, authorities said.
The H5N1 virus has killed more than 190 people worldwide, according to the World Health Organization.
The disease is hard for humans to catch, but experts fear it could mutate into a form that spreads easily between people, potentially sparking a global pandemic. To date, most human cases have been traced to contact with infected birds.