"It is the view of the ANC that the Office of the Public Protector has done its work which it referred to Parliament for further processing," spokesman Zizi Kodwa said in a statement.
"Towards this end, Parliament has established a Parliamentary Ad-hoc Committee which will refer to all reports submitted to be able to discharge its mandate."
Kodwa was responding to media reports on Sunday that Madonsela expressed concern that Zuma was second-guessing the recommendations she made in her report on Nkandla, titled "Secure in Comfort".
City Press reported that Madonsela wrote a letter to Zuma noting that in his 20-page reply to her report he did not address her findings or remedial action.
In his reply Zuma indicated Police Minister Nathi Nhleko needed to determine if he should pay back any of the R246 million spent on security upgrades at his Nkandla, KwaZulu-Natal, homestead.
"I am concerned that the decision you have made regarding the police minister gives him power he does not have under law, which is to review my decision taken in pursuit of the powers of administrative scrutiny I am given... by the Constitution," Madonsela wrote in the letter to Zuma, according to the newspaper.
"As I have already indicated, reports of the public protector are by law not subject to any review or second-guessing by a minister and/or the Cabinet."
Her findings and remedial action could only be set aside by a court of law, she wrote.
Kodwa said the letter by the public protector could be interpreted as undermining the Parliamentary process, and its authority to process the matter.
"It does appear that while the Public Protector has submitted her report to Parliament she has no confidence in the institution and its independence as the arm of state," Kodwa said.
"With reluctance, we suspect that the Public Protector has dealt with the investigation as a personal matter outside of the Constitutional mandate of the office."
The African National Congress called on the public protector to stop playing to the gallery and respect other constitutional entities to fulfil their role without interference and undue pressure.
"We are confident that Parliament and its committees will act in the interest of public good and we do not doubt their bonafides," Kodwa said.
"The extraordinary conduct of the Public Protector raises questions about her neutrality on this matter which might undermine the credibility of her conduct or the intentions of her report."
The ANC reaffirmed its belief in Chapter Nine institutions and their role to deepen democracy and accountability of government.
"We urge the Public Protector not to undermine the role of this office by her conduct which is contradictory to her recommendations that parliament must process her report and that of the President," he said.