Bermuda-registered Sea Containers delayed the publication of its annual report and warned it expected the document to include an "explanatory paragraph" from its independent auditors "raising substantial doubt about Sea Containers' ability to continue as a going concern".

The news whacked the shares, which plunged 30pc in New York from $4.89 to $2.13.

A Sea Containers spokesman insisted its mounting financial problems would have no impact on GNER, which is effectively ring-fenced from its parent.

"The franchise agreement is with GNER and Sea Containers is not a party to it," said Sea Containers spokesman Lisa Barnard, adding: "Sea Containers is not a guarantor of GNER's debt."

She declined to be drawn on what would happen if Sea Containers went under. However senior rail industry sources said such failure would trigger a change of control clause at the GNER franchise, prompting talks with the Department for Transport.

The DfT would be expected to review whether GNER had the sufficient financial strength to continue to run the franchise. As long as it was satisfied, the department would not be obliged to re-let it.

One rail source said: "If Sea Containers went bust that would be deemed a franchise change event and they would certainly have to go back to the Government which would ask if they were good for delivery. It's always been a concern with GNER because their parent company has a weak balance sheet."

GNER last year retained the East Coast franchise, operating between London, Leeds and Edinburgh, for the next 10 years with a blockbuster bid. It pledged to pay £1.3bn to the taxpayer in premiums over the life of the franchise.

At the time, Christopher Garnett, chief executive, said: "I would rather overbid and win than underbid and lose."

GNER is already in dispute with the Office of Rail Regulation after it was refused the right to start new London-Leeds services, while a competitor, Grand Central Railways, has been allowed to start new services on the East Coast tracks. GNER has threatened a judicial review, arguing the decision wrecks the financial calculations on which its bid was made.

Sea Containers, which admitted it was in breach of its banking covenants, is desperately trying to raise more cash through the sale of its Scandinavian ferry business Silja, which was put on the market with a price tag of ?600m (£415m). The auction may now turn into a fire sale.