The rail regulator commissioned KPMG to examine Network Rail’s management structure as part of a wider review of its licence to operate.

Rail-industry insiders expect KPMG to question how the company’s board is held to account and incentivised, and will propose more transparency on how management bonuses are calculated.

The Office of Rail Regulation declined to comment ahead of publication.

Network Rail, led by chairman Sir Ian McAllister and chief executive Iain Coucher, owns and operates nearly all Britain’s rail track and signalling, and most big stations.

It is a company limited by guarantee, meaning it has no shareholders. Instead the board reports to 118 “members”, some of whom represent railway- industry interests, and others who are members of the public.

The structure has been called into question several times, normally over the payment of bonuses to senior staff.

The pressure intensified earlier this year when over-running engineering works disrupted the travel plans of thousands over Christmas and the New Year.

At the group’s recent annual meeting members voted in favour of setting up their own inquiry into governance. It is understood that members will select a steering committee to run the inquiry, which will take on professional advisers. Network Rail will pay for the work. A report is expected by Christmas.

The renewed spotlight on how Network Rail is run comes as the company is in the final throes of negotiating with the regulator how much it will earn over the next five years.

Network Rail has asked for around £2.6 billion more than the regulator wants to give it, and says the watchdog’s efficiency targets are too tough.

Part of the settlement will be a change to Network Rail’s fundraising activities. To date it has borrowed using a government guarantee of repayment.

It is envisaged that from next April it will borrow on its own account.