The ITV Tonight documentary also contains claims by an executive who masterminded the original rail contracts system that the cost of the blunder will far exceed the £40 million estimated by Government.
Chris Stokes, former Deputy Director of Franchising at the Department for Transport said:
I would guess that bidders for other franchises will claim back the costs of their bids as well, so yes I think it’s likely that it may well be £100 million.
Government plans to take the West Coast Mainline away from Virgin were reversed earlier this month, after "serious defects" were found in the process.
Three civil servants have been suspended and two official reviews launched.