The accusations came as the Department of Public Enterprises criticised the inquiry into state capture taking place in Parliament and led by the committee for public enterprises for being "procedurally unfair".
He said it was Khoza who first put it to him that the minister is "captured", but his observations had borne out the theory that she is entangled in the dealings between Eskom management and the family reported to have skimmed billions off the State's balance sheet.
Brown echoed Ben Martins' statement earlier on Tuesday calling for fairness. "The swirl of allegations that has enveloped them must be investigated and set right".
"We understand that Eskom will be given an opportunity to make a formal presentation at the Parliamentary inquiry where it will give an honest, transparent and truthful account of events". She said Parliament must "level the playing fields" by giving all sides the platform to respond to the allegations.
Brown later released a statement describing the inquiry as a "kangaroo court" and reiterated that she doesn't take instructions from anybody.
"The acting [Eskom] chairperson has assured me that those responsible will be charged by the company", Brown said.
This came after Qoma accused Brown of lying and the continued woes at the power utility company.
Qoma said Brown's protection had also extended to Eskom's chief financial officer, Anoj Singh.
It alleged that evidence leader Nthuthuzelo Vanara had allowed statements to be made about people without them being given an opportunity to respond. He also denied he was with the Guptas, Duduzane Zuma and Salim Essa in July in Melrose Arch.
Martins said he attended the funeral service of late government spokesperson Ronnie Mamoepa in Pretoria before he went to the national executive committee lekgotla later that day. Khoza had told a "G-brother" of the impending suspension and he had, in turn, contacted Brown, who stopped Koko's suspension.
He has accused Brown of lying about everything.
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