Accounts filed with Companies House show that Ernst & Young raised doubts about the ability of Borders UK to continue as a going concern.
The bookstore chain was recently sold to Hilco, a fund that invests in British retailers facing difficulty.
The accounts, which refer to the year ending 2 February 2008, were signed off by Ernst & Young on 31 July this year.
The company said it had prepared the accounts on a going concern basis, but its auditors said it faced a number of uncertainties, including that it operated in an extremely competitive sector, and its sales performance would be difficult to forecast, the Financial Times reports.
Ernst & Young said: 'These events and conditions indicate the existence of material uncertainties which may cast doubt about the group's ability to continue as a going concern.'
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