The discovery, in the southern state of Styria, follows the detection of H5N1 in a dead cat in Germany last week.
That case was thought to be the first example outside Asia of the virus crossing species to infect a mammal.
However, it is unlikely the virus is spreading between cats and chances are negligible they may pass it to humans, says the BBC's Ania Lichtarowicz.
The virus has also spread for the first time to Poland, while Serbia says it has detected the strain in dead swans and has sent samples for further tests.
The H5N1 virus can be caught by humans who handle infected birds, but it is not yet known to have passed from one person to another.
However, experts fear the virus could mutate to gain this ability, and in its new form trigger a flu pandemic that could kill millions.
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