South Africa's International Trade Administration Commission (ITAC) had imposed the tariffs on Brazilian chicken products as it believed the imports were being 'dumped' or sold at a very low price, affecting the African country's own poultry sales.
"It makes it awkward for the two countries' existing friendship to be compromised by such an unreasonable attitude, totally lacking reciprocity with the trust that Brazil has placed in this relationship," said Brazil poultry association executive president Francisco Turra.
South Africa had imposed a duty of 62.93 per cent on Brazilian whole chickens and 46.59 per cent on boneless cuts.
The Brazilian Ministry of Development estimated that the South African measures cost its economy an additional US$70 million per year.
According to the Brazilian Chicken Producers and Exporters Association (Ubabef), while Brazil accounted for 73 per cent of South Africa's chicken imports, Brazilian poultry represented just 15 per cent of the chicken consumed in South Africa.
If the two countries are unable to resolve their differences within two months, Brazil's complaint will be referred to a WTO dispute resolution panel.
This has been the fourth case brought against South Africa's anti-dumping measures. None of the previous three cases brought by India, Indonesia and Turkey advanced to the panel stage.
India and Turkey did not press their disputes while Indonesia withdrew its complaint after South Africa dropped its protective measures.
Brazil is the world's largest exporter of chickens and chicken meat in the world, and the country has been targeting emerging economies to develop its industry.