Hidden in the small print of the deal negotiated with Railtrack by Virgin, controlled by Richard Branson, is a provision for a new Virgin service linking London and Edinburgh.
The plan would see Virgin, which by 2001 will have a train linking the two capitals with a journey time of 3 hours 50 minutes, competing head to head with GNER's east coast service which, at best, take four hours.
Christopher Garnett, GNER's chief executive, described the move as Virgin "cherry picking". GNER has proved phenomenally successful, beating the revenue British Rail raked in by more than pounds 30m since it took over in 1996, taking pounds 310m.
"Glasgow [Virgin's current main station] is 40 per cent larger than Edinburgh and Virgin runs a 35 per cent worse train service from there than we do from Edinburgh," Mr Garnett said.
GNER points out that it cannot respond in kind and "attack" Virgin's market on the west coast. "It is part of the deal to get the west coast modernised that there would be no competition from people like us," said Mr Garnett.
The huge investment by Railtrack and Virgin will lead to the introduction of fast tilting trains.
Mr Garnett pointed out that the regulator, John Swift QC, had only published "draft conclusions" and he would be lobbying hard to see changes.
Virgin said it was unperturbed by GNER's plans. "Nobody else has presented a business plan to Railtrack for this type of project," said a spokesman.
Mr Swift said the plan had to be sensitive to the needs of the railway as a whole. "I want to see further improvements to services to Glasgow and Edinburgh and a significant improvement to services to North Wales," he added.