Agriculture, Forestry and Fisheries Minister Senzeni Zokwana told journalists in Cape Town that they were doing everything possible to contain the spread of the disease.
Bird flu has been reported in 47 countries, in Africa, Asia, the Middle East and Europe.
The South African Poultry Association (Sapa) said more than R50m had already been lost, with thousands of chickens culled and farms left scrambling.
On the other hand, the South African Ostrich Business Chamber said it had not felt the impact of the outbreak, but was keeping a close eye on developments.
The first case of bird flu was detected on a farm in June. Since then several cases have been reported.
“Government veterinary services, together with the poultry industry, have worked tirelessly to curb the spread of the disease by destroying all infected poultry,” said Zokwana.
He said the current strain did not cause the disease in humans.
Sapa chairperson Achmat Brinkhuis said they had not yet done a full assessment of the economic impact on the poultry industry, but that it had caused big losses to breeding farms.
Brinkhuis said the estimated loss was around R50m.
Piet Klein, the chief executive of the South African Ostrich Business Chamber, said they'd had no fatalities among ostriches. However, in 2011 a similar outbreak had cost the industry R1.2billion.
“At the moment we are not counting ostriches. They have got their own protection against the viruses,” said Klein.
More than 2.1million chickens have been affected by the outbreak.
Zokwana denied that they had been slow to respond to the outbreak since the first case was reported in June.
He said they had been on the ground from day one with control measures. “We have worked well with the industry, and they have been able to co-operate,” he said.
Some of the bio-security measures being proposed on farms include keeping poultry away from wetlands and areas frequented by wild birds, not providing food that would attract wild birds, and to control people’s access to places with poultry.