German authorities on Saturday announced that tests on a number of ducks from the farm at Wachenroth near the southern city of Erlangen, 200 kilometres (120 miles) north of Munich, confirmed the strain, adding that 160,000 poultry would be destroyed.
German and EU officials discussed the problem in Brussels on Monday and the Commission in a statement declared itself "satisfied" with the emergency measures taken.
The buffer zone is drawn around towns and hamlets and is not a perfect circle, European Commission spokesman Philip Tod explained.
It is however larger than the required protection and surveillance zones (three and 10 kilometres) which are routinely applied in such cases.
In the buffer area, restrictions on the movement of poultry will apply but culling is not deemed necessary.
The measures will be reviewed next month in light of the success in dealing with the outbreak.
H5N1, which in its highly pathogenic strain can also infect humans, sometimes fatally -- was found in other ducks in Bavaria this month and over the summer around 50 wild birds were found dead with the virus across the country.
Wild birds can infect domesticated birds with the highly pathogenic strain. Experts fear it could mutate into a strain that can be transmitted between humans.