Mkhwebane gave notice five months ago that she would indeed oppose Zuma's ongoing legal challenge, saying the reason for this was to comply with court rules.
She wants the Constitution to be amended to ensure that the mandate of the Bank promotes economic growth and not only protects the value of the rand exchange rate.
Absa has noted the Public Protector's statement today regarding her investigation into the SA Reserve Bank's assistance to Bankorp between 1985 and 1995.
"We will continue to honour our constitutional mandate and the trust placed in us by the South African society". We will work side-by-side with the Public Protector.
Economists Nic Borain and Jeff Schultz at BNP Paribas South Africa said in a note that the Public Protector had placed the future of the central bank's autonomy into question.
"I am opposing the review by the President, including the Minister Zwane and Minister van Rooyen's applications because remember, they've also applied for judicial review to set aside the whole report", she further said.
Mkhwebane made the comments at a briefing in which she also ordered a re-opening of investigations into apartheid-era transactions between the state and Absa Bank.
Public Protector Busisiwe Mkhwebane in January reopened a probe of Absa, a unit of Barclays Africa, following a wider report published last November by her predecessor.
In December Zuma, who has denied wrongdoing had asked the High Court to set the report aside.
The preliminary report found that Absa - which took up ownership of the Bankorp group of banks - could be forced to pay back R2.25-billion to the fiscus after an unlawful apartheid-era bailout of banks in the Bankorp group. Zuma said he wasn't given enough opportunity to respond to the report prior to its publication, and that only he had the right to appoint judicial commissions.