Spokesperson Kgalalelo Masibi said in a statement that claims made by Madonsela's deputy, Mamiki Shai, in a Sunday Times report were baseless.
Shai claimed Madonsela changed findings on a report into the DA-led Midvaal Municipality and deliberately withheld the report's release until after municipal elections had been held.
"It is not true that the public protector changed findings on the Midvaal report willy-nilly," Masibi said.
"The statement that the report was delayed until after the local government elections is misleading and malicious."
Rather, Madonsela viewed the draft report and decided a more in-depth investigation was needed. This led to the report being delayed.
"It was under the public protector's hand that a more thorough investigation was done and many allegations substantiated."
Madonsela had not acted against a senior official reportedly accused of fraud because the person had been cleared of wrongdoing by the inspector general of intelligence, she said.
The Sunday Times reported that Shai also claimed Madonsela sought to change good governance recommendations which had criticised her conduct.
Masibi said Madonsela was of the opinion that Parliament was already appraised of the committee's findings and therefore all that was required of her was to respond to the matter.
"The public protector is not aware of any constructive criticism she was dismissive of."
In the newspaper report, Shai alleged that Madonsela took up cases beyond her jurisdiction, and hired external consultants to handle cases.
Masibi said: "It is not true that the public protector takes up cases that fall outside her remit".
"Should anyone know of a case the public protector took that is outside her jurisdiction, the [public protector] eagerly awaits such information."
Some investigations were contracted out due to a heavy backlog at the end of 2011/2012, but the decision was taken through the executive committee and in consultation with the national treasury, Masibi said.
"The public protector wishes to place on record the fact that all key decisions in the public protector South Africa are made through a memo system that originates from a relevant technical unit and goes through the chief financial officer, the CEO and the deputy public protector."
Madonsela welcomed Parliament's decision to assign the justice portfolio committee to look into various allegations against her and her office in a series of anonymous letters.
She requested the probe in July.
On Saturday Madonsela found out "with much surprise" that Shai was one of the authors of the anonymous letters, Masibi said.
Criticisms against the public protector are nothing new with several instances of aggrieved parties accusing her of bias.
The public protector's mandate is a wide one. Any citizen can ask for an investigation into allegations of maladministration, unfair or improper conduct, undue delay, or improper enrichment at any government body or public entity.
Once she had rescued the office from obscurity, Madonsela quickly became the go-to girl for anyone who has hit a government wall of denial and obfuscation.
In May this year the public protector's office was in the process of investigating 11 945 cases; a mixed bag of complaints about service and conduct failure, basic service delivery grievances against municipalities, social grants problems, identity documents problems, workers' compensation, RDP-house matters and allegations of maladministration involving the use of state resources.
And that's just the small stuff. Can't fathom why the KwaZulu-Natal health department will persist in using an expensive and dangerous medical device to do mass circumcisions? Call on the public protector.
Think perhaps Julius Malema may be involved in corruption and tender fraud in Limpopo? Worried about the textbook scandal in that province? Have a problem with the glacial pace in building RDP houses? What about the complete chaos in an Eastern Cape district municipality? Education crisis in Kuruman? Corruption in the hosting of the Miss World event? A probe into a conflict of interest involving the communication minister's and the hosting of an ICT event? Got questions about urban tolling?
Bring it on. And now Nkandla. All this with an investigative staff of about 130 and a full complement of just 300.
No wonder Madonsela has appealed for a bigger budget. R174-million is simply not enough to go around.
Without fear or favour
The reliance on the public protector appears to stem as much from the office's reputation for investigating without fear or favour as it does from the state's abysmal record in solving its own problems.
When the farce at the Limpopo education department – predicted in education circles last year already – came into the public eye, a handful of task teams were sent out to investigate. And when the problems of the platinum industry, which have been bubbling under for years, messily exploded across global news channels, understanding the context in which mining operates and miners live and work was outsourced to a commission of inquiry.
Not surprising then, given the public disarray of so many state departments and the mining sector on which our economy is built, that the rand has plummeted to a three-year low.
Third parties in general have become the thin blue line between public faith in government process and outright graft and incompetence. If it is not Madonsela we seek out, we turn to NGOs and the courts when the state turns a deaf ear to public pleas.
Parliament should rightfully be the forum in which citizens' representatives hold the state to account for its actions. But government is filled with yes-men who are dependent on their political principals for a seat and salary.
Question and answer sessions with the president are smattered with "sweetheart questions".
In one sickening exchange at the last Q&A with the president, one ANC MP used valuable question time, not to hold his president to account on behalf of his constituents but to ask: "Is it not true, comrade president, that the creation of the rural development department was a decision of the ANC in its comprehensive strategy to improve the conditions of rural people?"
Nevermind the failures of rural development or the scandal about the investment in a town just a stone's throw away from Zuma's own home, the president's response was: "Yes, it's true because this organisation cares for the poor, particularly those in the rural areas."
In another exchange, an ANC MP asked the rhetorical question: "Is it not only proper for all of us to wait for the outcome of the [Farlam Commission] inquiry instead of pre-empting?" to which Zuma responded, "I think it is very proper that we should wait for the commission of inquiry."
It's moments like these that make citizens cringe at the ineptitude of Parliament, the unhelpful self-congratulatory tone of a body that has failed to impress.
When the Democratic Alliance's parliamentary leader Lindiwe Mazibuko asked Zuma to justify the spending of R2-billion on the Nkandla Smart Growth Centre – known as "Zumaville" – while other nearby areas were without the most basic services like water and sanitation, Zuma appeared to deliberately misconstrue her question, and in a skilful dodge told Mazibuko, who he referred to as "my dear" and "ntombazana" (girl) rather than "honourable member" as is customary in Parliament, responded: "Why should people at Nkandla, 3km from where Zuma stays, starve? Why must they be isolated? Why should others who are in other areas be more important than those? Should they be punished because they are neighbours of Zuma? I don't think so."
With this quality of accountability from the top it is no surprise that some ministers simply refuse to answer written questions from Parliament, and director generals simply fail to pitch up when called to account to Parliament.
Independent analyst Collette Schulz Herzenberg, formerly of the Institute of Security Studies, said the whole point of question time is to have oversight over executive actions, particularly budgetary and service delivery issues.
In other countries, members of the executive can expect to be taken to task by members of their own party, who are accountable to their constituency.
But in South African the more difficult questions for executive members come from opposition parties, and this allows the ruling party to dismiss them out of hand.
"Because of the fact that only opposition parties use question time, it's come to be equated with attack politics or oppositions politics. Although question time is an opportunity to defend government's track record, it must also be regarded as a way for all legislative members to hold government accountable."
Shulz Hartzenberg said the sweetheart questions by ANC MPs were a form of "affirmation politics" and were a misuse of question time.
"[The time] should be used to ask pointed, direct questions to the executive and to get pointed direct answers, not to affirm each other," she said.
Adam Habib, deputy vice-chancellor of the University of Johannesburg, blames the state's inertia when it comes to resolving problems internally on an "accountability deficit".
"Politicians anywhere in the world deliver because of the threat of losing power. That's what democracy is. The incentive for politicians to deliver is because you'll get kicked out during the next election. That problem doesn't exist in South Africa," he said.
Tied to this is the problem of conflicts of interests – where ministers are involved in both politics and business – and deployment.
"If there are consequences to failures of delivery, people start making choices about the proper people to get delivery," he said.
Professor Susan Booysen, in the Graduate School of Public and Development Management at Wits University, said it is only strong political will and leadership that can overturn the "statewide affliction" that is the utter failure of internal controls, which has seen civil society, rather than government itself, holding politicians to account.
Booysen said it is in the ANC's long term interest to root out poor leadership at all levels of government.
"If they are seen to be walking with – and working with – people all the way they would be seen to be retaining credibility. Instead we see so much distance and disdain," she said.
Nowhere is this disdain seen more clearly than in Zuma's declaration that he has "sleepless nights" worrying about people who are still living in squalor 18 years after the dawn of democracy.
Apparently the fact that the R238-million bill for the "security" upgrades to Nkandla could have built over 4 300 RDP homes, or 450 school libraries, or according to MassMart CEO Grant Patterson built three Makro stores, do a R3-billion a year turnover and employ over a thousand people, was lost on the president.
As for leadership from the top, it is telling that despite the public's disgust at the spending, Zuma has yet to say anything on the matter, leaving it instead to his spokesperson Mac Maharaj to defend the move in a British newspaper. – Additional reporting by Sapa