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Infected ostriches were found on a farm near Albertinia and on two farms near Heidelberg two weeks ago.
All birds found on an infected farm had to be killed as part of the government's "stamping out" policy.
The industry had recently stated it had brought the H5N2 disease in the province under control and was a step closer to having its export status re-instated. The European Union had banned all exports since last April.
'It's a terrible thing for the whole industry," SA Ostrich Business Chamber CEO Piet Kleyn told the newspaper.
"We have to look at other control measures because this stamping out is possibly not the way to go."
