Pre-tax profit dropped to ВЈ1.52bn for the 12 months to 31 March, from ВЈ1.59bn a year before, while net debt climbed to ВЈ22.3bn from ВЈ19.7bn.
NR invested ВЈ4.7bn in the network, up from ВЈ4bn in the year before, and completed the ВЈ9bn upgrade of the West Coast Main Line.
However, the operator failed to meet targets for efficiency savings set by the Office of Rail Regulation.
Recently, chief executive Iain Coucher announced he was giving up his annual bonus this year, although he will still receive his long-term performance bonus.
Last year he was awarded a bonus of more than ВЈ305,000 and a further ВЈ205,000, despite the company being fined a record ВЈ14m by the ORR for three engineering work overruns during the 2007-08 period.
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It will not be clear whether other directors will give up their bonuses until the publication of Network Rail's annual report at the end of the month.
Better news came with punctuality hitting a new high, with 90.6% of trains arriving on time, the best performance since records began in 1992.
Trains are considered to have arrived on time if they are within five minutes of their scheduled time on commuter routes and within 10 minutes on longer routes.
