Virgin Trains services between Manchester Piccadilly and London Euston could end after the government barred the operator from bidding for the new West Coast Partnership franchise.
Virgin said it was 'very disappointed' by the Department for Transport's 'unexpected decision' and said it was 'carefully studying' the detail.
Virgin Trains, a joint venture between Virgin Group and UK transport giants Stagecoach, and has run its Pendolino trains on the West Coast Main Line route since 1997.
Bids were invited as part of a competition to run the new franchise as well as the new East Midlands and South Eastern franchises.
The operator of the West Coast Partnership franchise - a new franchise which will combine the current InterCity West Coast services with the development and introduction of HS2 services - is due to be awarded in June.
The winning bidder will be responsible for services from March 2020, and designing and running the initial HS2 high-speed services from 2026.
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Virgin Trains' entry comprised a joint bid by Virgin, Stagecoach and SNCF, France's national state-owned railway company.
But Stagecoach said it was informed by the DfT that it has been banned from the three franchise competitions after submitting non-compliant bids 'principally in respect of pensions risk'.
The DfT claimed Stagecoach 'breached established rules' - and insisted the company was 'responsible for their own disqualification'.
The East Midlands franchise meanwhile was awarded to Dutch company Abellio.
Stagecoach chief executive Martin Griffiths said: "We are extremely concerned at both the DfT's decision and its timing.
"The department has had full knowledge of these bids for a lengthy period and we are seeking an urgent meeting to discuss our significant concerns.
"We have drawn on more than two decades of rail experience and worked in partnership with local stakeholders to develop high quality proposals to improve each of these rail networks."
In a statement, Virgin Trains said: "We’re very disappointed by the DfT’s unexpected decision. We’ve led the industry for more than twenty years with our ground-breaking innovations, such as automatic delay repay, and award-winning customer service.
"We're studying the DfT’s decision carefully to understand why they’ve taken this action and would like to reassure all our customers that they can still book and travel as normal."
The DfT's decision to award the East Midlands franchise to Abellio means three out of five train journeys in Britain will soon be on services run by foreign companies or governments.
The 400-mile West Coast Main Line connects London to major cities including Manchester, Birmingham and Glasgow.
