It is the first case of the highly pathogenic avian influenza at a farm in the European Union this year, although in February there was a confirmed outbreak among wild birds in Britain.
The H5N1 strain which first emerged in Asia in 2003, has caused some 245 deaths in humans since then, with Indonesia and Vietnam among the worst hit countries, according to World Health Organisation figures.
Scientists fear that H5N1 will eventually mutate into a form that is much more easily transmissible between humans, triggering a global pandemic.
The German authorities informed Brussels on Thursday of the outbreak in Saxony, near the Polish border, and have set up the required "risk areas" around the outbreak, the commission said in a statement.
The German authorities have also culled all poultry on the farm including some 1,350 geese and ducks and 65 chickens and turkeys.
The commission said the Germans had applied all the necessary measures to deal with the outbreak, including setting up a three kilometre radius protection zone -- with very strict rule on entering and exiting of animals and people -- and a wider 10 kilometre surveillance zone.