Official figures that show 90 per cent of trains are running on time are highly misleading, it has been revealed.

In some cases the proportion of trains arriving on time is almost 25 per cent less than claimed.

Train companies are allowed to record a long-distance service as having arrived on time even if it was 9 minutes and 59 seconds late. Commuter trains and regional services can arrive 4 minutes and 59 seconds behind schedule and still be listed as on time.

Some companies argue that passengers do not mind short delays, even though a late arrival by a few minutes could mean them missing a connection and having to wait an hour.

Network Rail, the infrastructure company, believes that by recording every delay, however small, passengers would be given a more honest picture of punctuality, and overall performance would be improved. It has begun an experiment with South West Trains (SWT), Britain’s biggest train company, in which it records every delay, including those of only a few seconds.

It has found an alarming discrepancy between what it describes as “right-time arrivals” and the public performance measure (PPM), which is published every quarter by the Office of Rail Regulation.

Last month the PPM for SWT was 93.5 per cent, but the proportion of trains that actually arrived at exactly the right time was only 71.6 per cent.

Iain Coucher, Network Rail’s chief executive, told The Times: “For us to keep improving punctuality, we need to look at the causes of all delays, including the short ones. We can deliver an ultra-reliable railway by sitting down and working out why each train was not bang on time. It is our intention to do this across the network.”

Mr Coucher said that Network Rail would also start measuring whether each train arrived on time at intermediate stations. The PPM records only when trains arrive at their final destination. A long-distance train may run late for much of its journey but still officially arrive on schedule after accelerating on the last leg.

Mr Coucher said that increased pressure on train companies to ensure their trains were precisely on time would release spare capacity, allowing extra trains to be scheduled. “The right-time railway will show where there is surplus time, including when trains regularly arrive early and then sit at stations,” he said.

The average train last year on the 220-mile (350kilometre) Tokaido Shinkansen line, linking Tokyo, Nagoya and Osaka, was only 18 seconds late. By contrast, almost a quarter of trains on First Great Western’s high-speed service were at least ten minutes late last year.

Anthony Smith, chief executive of Passenger Focus, the rail watchdog, said: “Passengers expect the timetable to be a work of fact, not of fiction. We think the industry should adopt a new approach where ‘on time’ means ‘on time’.”

Richard Bowker, chief executive of National Express, which operates the East Anglia and East Coast franchises, said that he would be willing to publish the percentage of right-time arrivals if the media made it clear that delays were far worse by air and road.

Airlines allow themselves an even greater margin than train companies, with a flight not being listed as late if it arrives within 15 minutes of the scheduled time.

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