Network Rail chief executive Iain Coucher has announced that he will not take an annual bonus this year.
But he will still be eligible for a possibly substantial bonus as part of the Network Rail (NR) long-term incentive plan.
And other top directors of the rail infrastructure company are expected to take annual bonuses as well as the long-term bonus.
Last year, Mr Coucher received a £305,000 annual bonus as well as more than £200,000 under the long-term incentive plan, with the awards being based on NR's performance on meeting certain targets.
The bonuses were paid out despite NR being fined a record £14 million for three serious engineering overruns over the 2007/08 Christmas and new year period.
NR's remuneration committee is due to announce this year's bonuses shortly.
Last year, NR paid out £55 million in bonuses, with all staff receiving at least £871. The NR targets are set by the Office of Rail Regulation (ORR) and relate to train punctuality, how well NR has looked after the railways and the extent to which the company has made savings.
But the ORR has no direct influence on bonuses, which are a matter for the NR remuneration committee.
Gerry Doherty, leader of the Transport Salaried Staffs Association rail union, which has been campaigning for all bonuses to be scrapped for all NR directors, said: "I am pleased that Iain Coucher has finally bowed to the inevitable and listened to what (Rail Minister) Lord Adonis, the ORR, ourselves and the public have been saying for the past four months.
"There is never any justification in paying bonuses for running a state monopoly and, in view of the chief executive's £500,000-a-year salary, there is even less justification this year, given the public outcry over bonus rewards for failure."
