Five other top NR directors will be getting bonuses of between £59,000 and £67,000, the company announced.
Chief executive Sir David Higgins and his fellow executive directors could have been awarded annual bonuses of up to 60% of their annual salaries if all performance targets had been reached.
But with the company failing to meet some targets, including its trains-on-time target , the top bosses have got bonuses worth only 17% of their salaries. But this still means that Sir David, who is on an annual salary of £577,000, will get a bonus for 2012/13 of £99,082.
Group finance director Patrick Butcher, who is on a salary of £394,000, will get a bonus of £67,658, with network operations managing director Robin Gisby and infrastructure projects managing director Simon Kirby both getting bonuses of £63,708. Paul Plummer, the company's group strategy director, is being awarded a bonus of £59,759.
Where NR did particularly well was in meeting its passenger satisfaction bonus target of 84.3% but the company failed to reach its financial efficiency and asset stewardship targets.
NR chairman Richard Parry-Jones said: "2012 was a year of positive progress for the company with some great highs - delivering seamless transport for the Olympics - to lows of frustration with a slowdown in our rate of delivering better train punctuality. While this was particularly impacted by a year of extreme weather, the wettest on record, we are working to improve the resilience of our network to cope with such demands."
He went on: "The remuneration committee felt that while performance was good in most areas, truly exceptional performance had not been achieved in financial efficiency and asset stewardship, and our train performance targets were not met. But we also needed to recognise the significant successes that had been delivered in the business during the year."
Shadow transport secretary Maria Eagle said: "Ministers must now act and make clear that bonuses on this scale are simply not appropriate in a company that receives nearly four billion pounds of taxpayers' money every year. At a time when people are struggling to make ends meet, this out-of-touch decision will simply add to the growing feeling that we need real reform to the way the rail industry operates in Britain."