About half of Network Rail's income comes from government
Unions and MPs from all parties have questioned Network Rail's decision to pay £55m in staff bonuses.
Chief executive Iain Coucher will get a total of £510,581, despite presiding over engineering delays that stranded thousands of passengers over New Year.
Cabinet minister John Denham said the decision "raised an issue" over performance-related bonuses.
Network Rail said the bonuses were justified because more trains were on time, and delays were decreasing.
In addition to his £500,000 annual salary Mr Councher is to receive £305,581 as his annual performance-related bonus, along with an additional £205,000 under a separate three-year long-term incentive plan.
Two other directors of Network Rail will each receive total bonus packages of more than £350,000 each.
All other staff will get an annual bonus of at least £871, with £55m being paid out in total - about twice the amount awarded last year.
On Friday, Mr Denham, Secretary of State for Innovation, Universities and Skills, said that there was "no point" in having performance-related bonuses if they failed to take into account that only half the job had been done properly.
He said: "Whether people should get performance bonuses of that scale when there have clearly been very significant problems I think raises an issue that comes up too often with performance bonuses."
Louise Ellman, the Labour chairman of the House of Commons Transport Select Committee, described the bonuses as "outrageous and showing contempt for the public".
She added: "The travelling public will feel outraged, as I do, that they are awarding themselves these bonuses."
The Conservative transport spokeswoman Theresa Villiers said she was "astounded" at the size of the bonuses.
She added: "Although there is some good news in the report of the company's activities this year, the engineering over-runs at the New Year were a fiasco for thousands of passengers."
Liberal Democrat transport spokesman Norman Baker said: "This is money that will have been taken from the Network Rail investment pot, and should instead be invested in the railways."
Bob Crow, leader of the RMT transport union, said: "Once again we have Network Rail management showing that there's one rule for those in the big house and another for everyone else."
Network Rail's remuneration committee chairman Jim Cornell decided to back the bonuses, despite a formal letter last month from the Office of Rail Regulation (ORR) which pointed out his firm's performance deficiencies.
In February the ORR fined Network Rail a record £14m after engineering work on the West Coast Main Line over-ran during the Christmas and New Year period.
At the time, ORR chief Chris Bolt said that, while he was powerless to reduce the size of the bonuses paid to Network Rail bosses, he might press for a tightening up of the procedures by which bonuses were awarded.