The report found a that the R15.4-billion increase in the cost of the tender 'appears inexplicable, unreasonable and excessive'.
A draft report apparently says Molefe and Gupta associates misled the Transnet board into approving cost inflations on the locomotives deal.
A report, which City Press obtained, led to the resignation of three board members from the parastatal two weeks ago.
The former Eskom CEO's application for leave to appeal a ruling he pay back part of his pension payout failed on Tuesday.
The ruling comes after trade union Solidarity approached the high court to declare Molefe's controversial award of more than R30-million unlawful.
BLSA CEO Bonang Mohale said Brown did not understand Eskom's role in the economy.
Molefe's lawyer says he resigned "on the basis of early retirement".
“I have never denied I have met the Guptas.”
“I do not understand why we in Africa, who do not have electricity, are afraid of nuclear, or we are being made to fear nuclear.”
Molefe also said he had not received a R30.1-million pension payout, as had been widely reported.