At least 30,000 out of 140,000 chickens have died at a commercial poultry farm in the Paardeberg region in the Western Cape.
Western Cape Economic Development MEC Alan Winde says avian flu is not good for the economy.
He says avian flu is a bird flu type that has varying strains and is mainly transmitted through wild bird migration.
Earlier in the year, the Western Cape got its first avian influenza case in the ostrich industry in the Heidelberg region, where three farms were placed under quarantine, according to Winde.
Ostriches behave a little differently with the flu, they don't die. When it gets into chickens, it's a different story.— Alan Winde, Western Cape Economic Development MEC
Winde says once the flu gets onto a farm, you have to move in and cull because it highly contagious for animals but not for humans.
He says he is extremely concerned by the economic impact caused.
It is very difficult to control birds that fly over the farm. Our vets have been working very hard over the past couple of weeks.— Alan Winde, Western Cape Economic Development MEC
Winde goes on to say vets are working at affected farms, doing their best to manage the situation.
At the moment, the flu is unlikely to affect food and poultry prices, the MEC says.
Take a listen to the full interview here: