The highly contagious H5N1 virus was found at a premises near Alford on Saturday (11 December).
The birds on the infected sites will be humanely culled with a three kilometre protection zone put in place.
Officials say the risk to human health is low, but infected birds should not be touched.
Last week, the UK's chief veterinary officer said there was a "phenomenal level" of avian flu in the UK.
An Avian Influenza Prevention Zone (AIPZ) has been in place across the country since 3 November.
It was extended on 29 November, requiring all bird owners to keep their animals indoors.