And he said there would need to be timetable changes to improve punctuality in Scotland.
NR is not meeting its 92 per cent punctuality target for long-distance services and has to explain why to regulators.
He told the Commons transport committee there had been a huge growth in the number of trains on the network.
As many as 12 rail operators used the West Coast Main Line, with the line now so busy it had become “the M25 of railways”.
Sir David told the committee: “You could hit 92 per cent on long-distance, but you might have to regulate other services to achieve that. It’s complex. It’s a trade-off, it’s always a trade-off.”
He wanted a debate on the whole subject of trade-offs.
On Scottish services, Sir David told MPs: “I don’t think we can achieve the punctuality target with the current timetable.”
He said it would take about 12 months to modify the timetable.
The chief executive and top directors are giving up their bonuses, but are still in a management incentive scheme.
Asked if management incentives were appropriate for NR, Sir David replied: “You want to attract to an organisation people who are ambitious, who take risks. I believe performance-based pay and bonuses are part of that.”