Last week Switzerland's federal food safety office (BLV) began monitoring lakes in the country after more than 80 wild birds were found dead around Lake Constance of the H5N8 virus.
Over the weekend, two wild birds were found dead on Lake Geneva, said the BLV on Tuesday.
Currently the highly contagious virus has only affected wild birds in Switzerland but the fear is it could spread to domestic poultry in the country, after cases were reported on chicken farms in Hungary and Austria.
On Tuesday the BLV said it was stepping up its safety measures and that from Wednesday the whole country would be monitored.
Restrictions will now be placed on all domestic birds living outdoors in order to prevent contact with wild birds, the BLV said in a statement.
Domestic poultry must now be fed and watered indoors, in a place that wild birds cannot access.
Chickens displaying symptoms of potential bird flu should be kept separately from other birds, it added.
The H5N8 virus is transmitted by birds on migration routes south for the winter.
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.