Engineering overruns at New Year caused chaos on many rail services
Network Rail chiefs could see their bonuses cut after a report commissioned by rail regulators suggested a raft of sweeping changes.
The report suggests amending the firm's bonus scheme and making it easier for board members to be dismissed.
Customers and politicians have criticised the fact that executives got their bonuses despite engineering work overrunning, and causing problems.
Last month, Network Rail decided to set up an enquiry into how it has been run.
Network Rail runs the UK's rail infrastructure, and instead of shareholders is controlled by "members" who are drawn from the rail industry and general public.
The board of directors are held to account by the members.
Earlier this year, Network Rail announced that its top three executives would receive bonuses running into hundreds of thousands of pounds, despite public anger over cancelled and delayed journeys during the new year.
Two executives received bonuses of more than £200,000, while chief executive Iain Coucher pocketed more than £305,000.
Furthermore, as part of a separate three-year incentive plan, two of the executives got an additional £153,000, while Mr Coucher received £205,000.
Network Rail has already been fined £14m by ORR for the various overruns, one of which was at Rugby and caused chaos on the West Coast Main Line.
The report into Network Rail was carried out by KPMG at the request of the Office of Rail Regulation (ORR).
In its report KPMG said that Network Rail's members had raised concern that executive remuneration did not follow an agreed process.
Among its conclusions, KPMG suggested forcing the board to write a public letter to explain cases where the firm had underperformed.
However, KPMG said that while most members were motivated by "sound intentions", others felt some members could be "influenced" by Network Rail's management board.
ORR chief executive Bill Emery said that he welcomed the report and it would help ORR to decide whether to make changes to Network Rail's licence condition on corporate governance.
Network Rail said it would "welcome any positive proposal that supports Network Rail's board - accountable to its members - to continue with its objectives of exercising best practice in corporate governance."
The company added:
"Network Rail has achieved much since it took over from the failed former licence holder, Railtrack. Our not-for-dividend model has delivered year-on-year improvements for passengers and freight operators...Network Rail has cut the costs of operating and maintaining the railway."
Bob Crow, general secretary of the Rail Maritime and Transport union, said the bonuses received by Network Rail bosses had been "grossly unfair" and said it would be "nothing short of obscene" if they received even bigger payouts while some staff were currently fighting to save their jobs in the face of budget cuts.
Gerry Doherty, leader of the TSSA rail union, also attacked the executive bonuses.
"It is high time we ended the fat controller bonuses at Network Rail where the bosses reap huge rewards regardless of performance failures," said Mr Doherty.
"There should be no reward for failure - only for improved passenger service," he added.