The senior management group at Glasgow University, including principal Professor Anton Muscatelli, have been awarded salary increases of up to 3.6% – compared to 1% for academics and support staff.
Salaries for lecturers are set on a UK-wide basis, but those of senior managers are agreed by a remuneration committee made up of lay members of the university's ruling Court.
The salary hike for the senior management group – which includes vice-principals, heads of college, the secretary of Court and the directors of finance, human resources and corporate communications – takes Mr Muscatelli's basic pay to more than £257,000.
Staff and students are particularly angry because they believe the university has not been well run in recent years.
Dave Anderson, president of the university's branch of the UCU union, said: "This decision to award a pay rise beyond that offered to the majority of staff leaves management open to charges of lining their own pockets and highlights precisely why university governance needs to be updated.
"Staff surveys have highlighted ongoing disaffection and daily pressures faced by staff, while our own survey put Glasgow in the top 20 of UK universities for workplace stress. With ordinary staff facing another real terms pay cut, much more needs to be done to recognise the role of staff across the institution."
Craig Angus, vice-president of the university's Students' Representative Council, added: "Many students have expressed concerns about the future of academic departments and staff appear to be under a huge amount of pressure. Although there have been positive developments at Glasgow, there is a danger that a decision such as this will create tension.
"It's common knowledge that money is tight so such a decision contrasts hugely with the messages about cutting back which are received by the wider population of the university."
However, a spokesman for Glasgow University said the increases came after several years where pay had been frozen.