The Western Cape Veterinary Service has warned avian influenza has been detected in two commercial layer farms in the Paardeberg area in the Drakenstein and Swartland Local Municipalities.
The first outbreak was confirmed last Friday and the second earlier this week.
Avian influenza is a viral disease spread by direct contact between healthy and infected birds or through indirect contact with contaminated equipment or other materials.
Western Cape Agriculture MEC Ivan Meyer says about 120,000 birds have died or been destroyed so far.
The exact strain is not known and is still being investigated.
Meyer says highly pathogenic avian influenza outbreaks were detected in poultry in other provinces in the last sixteen months.
The Western Cape has not seen the virus in commercial poultry since early last year.
At this stage there is no vaccine or treatment for highly pathogenic avian influenza, and because of this, current best practice in much of the world requires the culling of infected birds as quickly as possible to limit the spread of the disease.
Local farmers are urged watch for any signs of the disease.