The principal of Glasgow University accepted a £23,000 pay rise in the past year - an increase of more than five times the rate of inflation.
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The 11% increase brings Sir Muir Russell's salary and pensions benefits to some £234,000 a year at a time when the rest of the university's staff have been given increases of just 4%.
Two years ago, Glasgow University laid off hundreds of staff in order to balance its books and it took the controversial decision, on financial grounds, to pull out of a satellite campus set up to regenerate Dumfries and Galloway. The decision has now been reversed after intervention from the Scottish Government.
As convener of Universities Scotland, which represents university principals, Sir Muir, the former permanent secretary of the Scottish Executive, has also been openly critical of the tight financial settlement for universities.
Last year's university accounts show the level of Sir Muir's remuneration package jumped from £184,000 in 2004-05 to £211,000 in the last financial year - a 15% rise.
The latest increase is likely to make Sir Muir one of the highest-paid principals in the country, depending on the increases enjoyed by other university leaders which have not yet been revealed.
Last year, the highest-paid principals in Scotland were Professor Duncan Rice from Aberdeen University (£215,000), Dr Brian Lang from St Andrews (£209,000), and Sir Alan Langlands from Dundee (£202,000).
Terry Brotherstone, who is president of the lecturers' union UCU Scotland, said: "For the Glasgow University principal to be awarded, and to accept, an 11% pay rise soon after holding staff to a mere 13% over three years highlights the hypocrisy that the new managerial culture is bringing to universities, as to many other public and charitable institutions.
"This can only increase the cynicism of teaching and research staff, many of whom could earn more in the private sector if they were not dedicated to the job they do and the students they serve.
"There is a growing feeling that universities are being turned into businesses in which the collegiality on which their past successes have depended is abandoned and senior managers are paid inflated salaries to get as much as possible out of their junior employees for as little reward as possible."
A spokesman for the university said: "The salary of the principal is performance-related and reflects the responsibilities of running a large and complex organisation. It is set by an independent university committee.
"The increase reflects the considerable successes which the university has enjoyed in the past year. "
As part of his pension arrangements from his career in the civil service, Sir Muir, 59, will pocket a one-off payment of £215,000 when he turns 60.
He can also expect to have an annual pension of £65,000 waiting for him at age 65.