Speaker of Parliament Baleka Mbete has lambasted the judiciary, saying judges are often highly politicised and accusing them of being prejudiced against the ANC, The Times reported on Tuesday.
In response, the Office of the Chief Justice, Mogoeng Mogoeng said her comments were "deeply concerning"and could hurt the country.
Mbete told The Times that she had raised her concerns during a meeting with President Jacob Zuma, Mogoeng and National Council of Provinces chairperson Thandi Modise.
"When there is a case that affects someone from the ANC, those cases would find their way [into the courts] and if they end up in the hands of certain specific judges, forget it, you are going to lose that case. It has nothing to do with merit, correctness or wrongness. Some names pop up in the head already," she said.
Mbete said: "ridiculous because they are such mundane issues that are clearly and very obviously matters of detail of internal arrangements, which, in fact, ought to lie in the domain of the legislature".
She also said she did not understand why the opposition parties "seem to have a lot of confidence" that they would win in court.
Mogoeng's spokesperson, Nathi Mncube told The Times that the Chief Justice was concerned about "baseless perceptions or overly-generalised complaints against the judiciary and individual judges in particular".
"What the speaker, with the benefit of legal advice, ought to have done was to either lodge an appeal in every case where bias or an injustice is believed to have been committed or lodge a complaint with the [Judicial Service Commission] against the particular judges she believes are anti-ANC.
"The Chief Justice is not supposed to be the one to do it. There are constitutional and statutory mechanisms open to any aggrieved litigant.
"But, the Chief Justice wants to assure all South Africans and all litigants that the judiciary will continue to administer justice to all alike without any fear, favour or prejudice and only according to the constitution and the law," he said.