More than 10,000 ducks will be destroyed at two farms north of Melbourne after an outbreak of bird flu.

Health authorities would not say where the farms are located but maintain the low-strength influenza strain is not a threat to humans.

The virus was detected during a regular check.

Department of Primary Industry head of biosecurity Dr Hugh Millar says the ducks will now be killed and the farms will be decontaminated to contain the disease.

"It's precautionary, it's preventative and we're not dealing with a high-pressure disease situation such as we have seen throughout Asia," he said.

"It's not a public health issue. It's really not even an animal health issue, except we don't want these viruses persisting."

Dr Millar says the virus probably came from wild birds.

"It is the harmless, low pathogenic form, but we are jumping on this from a great height," he said.

The last reported case of bird flu in Victoria was in 1992.