Deputy Chief Justice Raymond Zondo has denied axed South African Revenue Service (Sars) commissioner Tom Moyane leave to cross-examine Public Enterprises Minister Pravin Gordhan, while one issue remains reserved for further "clarification".

"Any witness appearing before the commission may be cross-examined by a person, should the chair deem it necessary and in the best interests of the function of the commission," Zondo said in his judgment at the commission of inquiry into State capture on Tuesday.

"The true test is whether it is necessary, or if it serves in the best interests of the commission," he added.

Zondo found that the five themes presented by Moyane in his application failed to show how Gordhan had implicated him through his statement on allegations of State capture; and that he had failed to show why these themes would serve in the best interests of the work of the commission.

As a result, his application to cross-examine Gordhan was dismissed. Zondo does, however, intend to get further clarification on an issue involving National Treasury, where Gordhan alleged that Moyane had pressed charges against him with the Hawks relating to the so-called Sars "rogue unit" while he was finance minister.

The decision comes after the commission heard Moyane's application for leave to cross-examine Gordhan in March, after Gordhan implicated him in testimony in November last year.

Moyane's advocate Dali Mpofu said Moyane's cross-examination of Gordhan was important, News24 earlier reported.

Mpofu read from Moyane's submission: "Under this theme, my version is that Minister Gordhan's affidavit is more significant for what it omits, than what it says. The omitted facts will give a truer picture of the commission about what actually went on behind the scenes."

Gordhan's legal team, in response, argued that Moyane's bid was merely a means to rehabilitate his career through the inquiry into alleged state capture.

"Mr Moyane very explicitly tells you that he is here to rehabilitate his reputation and career prospects… he is asking for your help to rehabilitate his discredited name," advocate Michelle Le Roux previously argued before the commission.

Responding to Le Roux's submissions, Mpofu said, if anything was going to discredit the commission it was the idea that it was acceptable for Gordhan - "the boss" - to come before the commission and cast aspersions on Moyane - "the subordinate" character - but it was not acceptable for Moyane to defend himself.

Direction will be given to both parties regarding an issue relating to the National Treasury - both parties will be expected to make written submissions on whether Gordhan's submissions that by laying charges against him, Moyane did so with malice.

The inquiry continues on Tuesday, with former IPID head Robert McBride back on the stand.