Judge Joos Hefer ordered their advocate, Steven Joseph, to stop cross-examining Ngcuka on alleged power abuses before covering his clients' spy claim against the chief prosecutor.
This was after the commissioner had ruled that the spy claim and power abuse allegations against Ngcuka were linked.
He first had to establish whether national director of public prosecutions Bulelani Ngcuka was an agent for the apartheid government. If he did not make a positive finding on this, his probe into the power abuse allegations fell away, Hefer decided.
His ruling cleared up a long-standing difference of interpretation of Hefer's terms of reference between the different legal teams involved in the proceedings.
It implied that all power abuse allegations against Ngcuka not tied to the spy allegations were not for Hefer's commission to decide over.
The spy claim against Ngcuka has already been practically destroyed by refuting evidence before the commission. It should therefore be very difficult for Mac Maharaj and Mo Shaik's legal team to link their allegations that Ngcuka abused his official powers to their original spy claim.
Hefer's ruling on his terms came on Wednesday afternoon in the middle of lengthy cross-examination of Ngcuka by Joseph. His questioning had up till then had focused solely on alleged power abuses.
He suggested that the chief prosecutor's Scorpions unit was the only possible source of information that was leaked to the media about both Maharaj and Shaik's brother, Schabir.
Both are being investigated by the Scorpions. It has been alleged that Schabir bribed Maharaj during his ministerial term to procure contracts from his department.
Ngcuka testified that he ordered an investigation into whether someone from his office leaked information about Maharaj to the media. The result was inconclusive.
He speculated that Schabir himself leaked some of the information to the media in an effort to "drag" Maharaj into the criminal case against him.
His aim with this could have been to ensure political intervention (into the investigation against him), Ngcuka suggested.
He said he knew "for a fact" that "a number of things" had been leaked to the media by people other than his officers.
He was apparently referring to earlier allegations that Schabir himself leaked to the media the fact that Deputy President Jacob Zuma was linked to the investigation against him.
Earlier on Wednesday, Ngcuka denied both the spy and power abuse allegations against him. He said it had caused "incalculable" damage to the National Prosecuting Authority, which he headed.
He maintained that he was not at the commission to clear his name or prove his innocence, because there was no reason for that.
"The reason I am here is to defend an institution established by the Constitution the National Prosecuting Authority."
Ngcuka reiterated that the NPA would continue investigating, and, if necessary, prosecuting those who broke the law, "no matter how wealthy or powerful they might be".
He added that he never thought he would have to investigate or prosecute any senior member of the movement that had created South Africa's current political and moral order.
Hefer adjourned the proceedings on Wednesday afternoon until 8.30am on Thursday- Sapa
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