The University of Liverpool was more than £15 million out in its financial forecasts for the past academic year, accounts reveal.
The university had expected to end the year to July 2009 with a surplus of £2.3 million. However, when the accounts were collated an overall deficit of £13.2 million emerged.
Sir Howard Newby, Liverpool vice-chancellor, told a meeting of the university's senate in December that immediate action had been taken to ensure that such an "unsatisfactory" situation did not arise again.
"The director of finance had been replaced and the new director would address the situation as a matter of urgency," minutes of the meeting say.
Minutes of an earlier university council meeting note "the decision of the director of finance to bring forward his retirement".
The director, Michael Yuille, had been in post since 2004 and was a former chairman of the British Universities Finance Directors Group. He was replaced by Rob Eastwood, previously finance director at Brunel University.
Liverpool's financial statements say most of the deficit was due to lower than budgeted research income.
The university's director of research and business, Colin Cooper, left the institution less than a year after he was appointed in February 2009.
A university spokeswoman said research income rose 10 per cent in 2008-09.
Mr Cooper's role had been replaced with a new position providing "integrated research support service", she added.
Liverpool's accounts also blame "significant provision for pension liabilities" and redundancy expenses for the deficit: about 200 staff, most of whom were in non-academic positions, took voluntary severance last year at a cost of £3.98 million.
Sir Howard said that the unexpected deficit "would be absorbed within the university's very strong balance sheet and that it should not impact on the 2009-10 budget allocations to faculties".
Neither would there be any impact on the university's strategic objectives, he said.
The university is the latest of a number of institutions that have uncovered major errors in financial planning.
Last year, the University of Leeds admitted that its forecasts for 2008-13 were over-optimistic by £20 million per year, while the University of Cumbria significantly underestimated its deficit for 2008-09 (see story, right).
A spokesman for the University and College Union at Liverpool questioned whether senior staff pay may be partly responsible for the state of the university's finances.
Some 112 members of staff earned more than £100,000 last year, up from 88 the year before, and the university paid senior staff £324,000 in compensation for loss of office.
The university spokeswoman said that 67 of the higher-paid staff had NHS contracts.
She added: "The university has made a number of improvements to its planning, performance and budgetary processes and continues to implement improvements to ensure the systems are reliable and robust."
She also said that the university was expecting a £1 million operating deficit for the 2009-10 financial year but was "working to break even".