GNER's parent company Sea Containers, which is struggling to strike a deal with creditors in the US, is thought to be pressing the transport department to renegotiate GNER's £1.3bn 10-year franchise, after failing to hit revenue targets.

It has blamed the London bombings, energy costs, track charges, and last month the failure of a legal move to stop a new operator running trains on the route under the department's "open access" provisions.

However, an executive at rival bidder Virgin Trains, 49%-owned by Stagecoach, said GNER's bid last year has been its undoing and will now be a test for rail franchise policy.

Chris Gibb, managing director of Virgin Cross-country, said in Edinburgh: "Everybody is watching the GNER situation and how things might develop. If they renegotiate with government, that sends an interesting signal to the rest of the industry. It was a staggeringly ambitious bid, expecting massive revenue growth, massive cost reduction and paying a high premium to government."

There has been speculation that GNER outbid Virgin and Firstgroup by as much as £300m, while recent reports suggest that either operator would now love to get its hands on the franchise at a far lower price, should GNER be unable to continue.

Gibb said the episode highlighted the need for careful examination of the totality of franchise bids, not just the highest offer.

A spokesman for Sea Containers said: "We will be raising with the department the question of open access, which will be one of a number of issues in terms of trying to get better value from our contract."

GNER will argue that Virgin for instance has a management contract which gives it more protection from revenue shocks and from open access.

One industry source said: "There has been quite a lot of sniping over the fence between Virgin and GNER – there is no love lost."

Virgin's Megatrain budget services, meanwhile, have exceeded all expectations, according to Gibb. Launched two months ago with fares starting at £1 on selected services, Megatrain has already sold more than 100,000 tickets. Gibb said the offer was now set to be expanded. "It could conceivably become the cheap bucket shop way of making domestic rail journeys." He added: "I would rather have £1, and a customer who might travel with us another day and pay more."

Virgin recently submitted its bids to retain the Cross-country franchise next year.