Molefe told the inquiry into state capture in Parliament last night that the sale of Optimum coal mine to Tegeta was above aboard.
He also told MPs that he was never paid R30.1million in pension payout as has been reported, but got more than R7m.
He said this was part of the pension benefits from his Transnet job.
He said he had agreed to pay back a portion of the pension, but the matter will be resolved in the High Court next week.
“I did not receive R30.1m as is widely reported. I received a lump sum of R7m, of which R4.3m was paid by me from Transnet,” said Molefe.
“This whole matter of how much I owe the pension fund will be determined by the High Court next week,” he said.
He also questioned former Public Protector Thuli Madonsela’s report on the phone calls he made to the Guptas.
He said she denied him an opportunity to respond to the allegations in the State of Capture report.
“The report contained a series of observations and did not make findings. The public protector did not ask about the phone records. An important principle of our Constitution to be heard was denied to me by the public protector,” said Molefe.
“The public protector says I can be placed in a Saxonwold area 19 times. This is all what she says,” said Molefe.
Former non-executive directors at Eskom denied any knowledge of the links between the power utility and transactions with the Guptas.
Veroshni Naidoo, who resigned from the Eskom board last year, detailed how she was shocked by the R600m prepayment to Tegeta.
She said the money should have gone to business rescue practitioner Piers Marsden and not Tegeta to buy Optimum coal mine.
Naidoo told the inquiry in Parliament into state capture yesterday that nothing was said to them to suggest the money would be given to Tegeta.
He said the first time she heard of the R1.6billion guarantee to Tegeta by Eskom was during a media briefing and suspended Chief Financial Officer Anoj Singh answered media questions on it.
“We did not receive any assurance or give assurance to the guarantee.
"We could not approve the guarantee, because the threshold of the guarantee is R250m,” said Naidoo.
This was a similar issue raised by another former Eskom board member, Venete Klein, that she was surprised that executives could approve up to R750m in contracts.
Klein also agreed with former finance minister Pravin Gordhan that the R1.6bn guarantee was in violation of the Public Finance Management Act.
She also said that she did not know about the R1.6bn guarantee until it was raised in the media conference and Singh responded to the questions.
She said the only thing that served before their board was a R103m contract for McKinsey and it was for a corporate plan.