"There are a few who would have us believe the public protector's power is limited to making recommendations and leaving it to Parliament," she told reporters in Pretoria.
"I am not one of those."
Asked if she could go to court if her recommendations were not followed, she replied: "I can but I won't."
She said there was an African proverb: "You don't go to court together and return as friends."
That was why she discouraged ministers to do that with her reports.
"It's a waste of money."
She believed in dialogue and would ask for a meeting with President Jacob Zuma to discuss the way forward.
Her office has always had a good relationship with the office of the president and had the letter not been leaked, there would not have been an uproar.
"There has never been drama or lack of assistance from the presidency, but the drama arose due to the leaking of the letter. Had the letter not been leaked or commented on by outside actors, the president would have considered my letter," she said.
Madonsela was responding to the war of words that erupted between her office and the African National Congress. The fight emanated from a leaking of a letter she wrote to Zuma regarding his response to her Nkandla report.
Madonsela's report looked at the R246 million spent on security upgrades at his private Nkandla, KwaZulu-Natal homestead.
The ANC on Tuesday accused Madonsela of not doing her work correctly. Party secretary general Gwede Mantashe said she was abusing her office and trying to get media attention by saying things not in any report or being investigated anywhere.
This followed Madonsela's claim that the letter she had written to Zuma was leaked to the press by a senior ANC official.
In her letter she cautioned Zuma he was second-guessing her recommendations that he should repay part of the money spent on features at Nkandla unrelated to security, such as a swimming pool, cattle kraal, amphitheatre, and visitors' centre.
In his reply to her report on Nkandla, Zuma indicated Police Minister Nathi Nhleko needed to determine if he should pay back any of the R246 million.
Madonsela wrote in her letter: "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."
Mantashe denied the leak came from the ANC and said Madonsela's office had leaked every report she wrote and blamed it on the divisions within the ANC.
He suggested that she had worked with Julius Malema's Economic Freedom Fighters, whose MPs heckled Zuma about Nkandla in Parliament last Thursday.
Madonsela on Thursday called on external actors not to meddle in state affairs.