Mkhwebane summoned four former South African Revenue Service (Sars) officials to appear before her today in connection with her probe into the early retirement payout made to former Sars deputy commissioner Ivan Pillay.
Gordhan was finance minister at the time the payment was made to Pillay.
Pillay; former Sars commissioner Oupa Magashula; Sars head of legal Vlok Symington; and Minee Hendricks, former personal assistant of Gordhan, were due to be quizzed by Mkhwebane.
On Sunday, Mkhwebane maintained that she was not being used in political infighting in the ANC.
Former National Director of Public Prosecutions Shaun Abrahams dropped charges of fraud against Gordhan, Pillay and Magashula in relation to the payment to Pillay.
Their appearance comes days after Mkhwebane opened a criminal case against State Security Minister Dipuo Letsatsi-Duba, in which she asked the police to charge the minister for allegedly failing to furnish her with a copy of a report by the former inspector-general of Intelligence, advocate Faith Radebe, which allegedly corroborates allegations that Gordhan was involved in the setting up of a "rogue unit" at Sars while still commissioner.
Mkhwebane's spokesperson Oupa Segalwe said her decision to summon Pillay, Magashula, Symington and Hendricks was not politically influenced.
“The National Prosecuting Authority (NPA) was pursuing a criminal matter (on the Pillay payment).
"The Public Protector, on the other hand, is looking into maladministration or administrative lapses in the governance of organs of state, not criminal conduct.
"The public need to be able to distinguish between the two - the NPA and the Public Protector,” he said.
Segalwe said it was in the interest of those who are alleged to have engaged in wrongdoing to have their names cleared.
“Accordingly, any person whose conduct is reported to the Public Protector should welcome the opportunity to clear their names rather than to want to tarnish the integrity of our investigation by baselessly alleging 'factional battles'.
“If implicated parties are unhappy about the outcomes of a Public Protector investigation, they have a recourse in that they can take the matter to court for a judicial review.
"No one should be seen to be above scrutiny,” Segalwe said.
In November last year, Mkhwebane summoned Gordhan to appear before her on the Pillay matter.
Gordhan’s appearance came four months after he testified about the same matter before the Nugent Commission, which was probing governance at Sars while disgraced former commissioner Tom Moyane was still at the helm.
Gordhan told the commission in June last year that he had approved the early retirement of Pillay after he was satisfied with the investigations that Magashula had obtained a legal opinion on the matter.
After his testimony, Pillay, Magashula and Gordhan were charged with fraud related to Pillay’s early retirement.
They were served with a summons on October 11 2016, but Abrahams withdrew the charges later that month.
Abrahams said: "I am satisfied that Mr Magashula, Mr Pillay and minister Gordhan did not have the requisite intention to act unlawfully.”
On Sunday, Magashula confirmed that he was appearing before Mkhwebane, saying he had already submitted a founding affidavit to her office.
“The Public Protector is an important office of the land. My attitude is I've got to appear and explain what happened.
"If they think I can help, I got an obligation to answer to them. They were appointed by Parliament.
“I am going with that attitude. I am not going to prejudge them. I am going to answer to the best of my knowledge,” Magashula said.
He said he would be accompanied by his legal team, but they would be there only as observers.
“I will be talking and asking questions. I've co-operated so far. I gave them my founding affidavit.
"I hope to give them my supplementary affidavit after discovery of certain things,” he said.
Magashula was due to meet Mkhwebane at 3 pm and Pillay was expected to appear at noon.
It was not clear when Symington and Hendricks would appear.
Gordhan’s spokesperson, Adrian Lackay, said the minister would not comment on the ongoing investigations by Mkhwebane.