The first cases of the virus were identified in Mecklenburg-Western Pomerania in the northeast of Germany, and on the Bavarian side of Lake Constance in the south, where 80 wild birds had been found dead by Friday.
In parts of Germany, agricultural authorities have ordered that all poultry be kept indoors so that they do not become infected by wild birds.
The highly contagious H5N8 virus is transmitted by birds on migration routes heading south for the winter. The sub-type was first identified in Denmark.
Austria, Switzerland, Hungary and Poland have all also reported confirmed cases, meaning that the bird flu has spread to at least six European countries.
Robert Habeck, Minister for Agriculture in Schleswig-Holstein said though that the spread of the virus posed no risk to consumers.
Poultry is still safe to eat as long as people follow the usual hygiene procedures such as thoroughly washing cutlery and keeping meat separately from other foodstuffs, he said.
Switzerland's federal food safety office, BLV, says that there is no evidence the virus can be passed to humans. However, the BLV is advising people not to touch dead birds if they find them, and to tell the police.