Police in the southern state said restrictions on movement had been put in place around the Speichersee lake, east of Munich, after two out of three ducks found dead there were confirmed to have been carrying the virus.
Press reports said around 14 other birds had also been found dead in the area, but it was not known if they were infected with the virus, which is potentially deadly to humans.
More than 150 wild birds have died of H5N1 in southern and eastern Germany in the past few weeks, and a month ago the disease spread to a smallholding in the eastern state of Thueringen.
It was the first time this year that the highly pathogenic strain of avian flu had been found among domestic birds in Germany. Scientists have suggested it could have jumped the border from the neighbouring Czech Republic where it has infected poultry on large turkey and chicken farms.
A number of countries have banned poultry exports from Germany, which battled a widespread bird flu epidemic in 2006. The disease spread to mammals last year, infecting three cats and a marten.