The virus struck down a goose on a small holding in a forest near Wickersdorf in the eastern state of Thueringen where the owner kept four other geese and five ducks, the Friedrich Loeffler Institute said.
All the birds have been slaughtered.
It is the first time this year that the highly pathogenic strain of avian flu, which can also kill humans, was found among domestic birds in Germany.
It has infected wild birds in Thueringen and three other German states since late June.
The Friedrich Loeffler Institute has suggested that the disease could have jumped the border from the neighbouring Czech Republic where it has infected poultry on large turkey and chicken farms.
Germany battled a widespread bird flu epidemic in 2006.
The disease spread to mammals last year, infecting three cats and a marten, but it did not affect humans.