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.
Public enterprises minister Pravin Gordhan said the previous board did not take the allegations of corruption at Transnet seriously.
A report, which City Press obtained, led to the resignation of three board members from the parastatal two weeks ago.
Earlier this week, Gordhan lambasted the board for failing to act against officials implicated in corruption.
But Pravin Gordhan says he is not off the hook for his role any alleged wrongdoing.
Ramaphosa has ordered a Special Investigating Unit (SIU) to look into allegations of corruption at Eskom and Transnet.
Cash-strapped Denel owed its creditors millions.
HSBC reportedly picked up suspicious transactions related to the Guptas and their businesses.
The Guptas' fingerprints are all over an inflated IT contract.