Trouble at the top: Malcolm Gillies' departure from City University has revealed an intense relationship between governors and vice-chancellors

When news of the sudden "resignation" of Professor Malcolm Gillies broke this summer, there was astonishment all round. The former vice-chancellor of City University in London was well-liked and respected, popular with staff and highly regarded in universities for his thoughtful and imaginative approach.

He quit after a long-standing disagreement with the governing body – the university council chaired at present by multi-millionaire Apurv Bagri – about how to run the institution. An eminent music scholar, Gillies, 54, an Australian, had served less than two years as vice-chancellor. He will stay on as professor of music until next January and has been unavailable for comment since his departure.

His is not an isolated case. In recent months there has been a spate of such resignations, causing people to ask: who is running our universities?

At the University of East London (UEL), the former vice-chancellor, Professor Martin Everett, was first suspended by the governors, then went on indefinite leave and finally, earlier this year, "resigned".

Like Gillies, Everett had done nothing wrong. In a statement the governors said they made no criticism of his integrity or conduct, but that there had been an "irretrievable" mutual breakdown in trust and confidence.

In January this year it was announced that the vice-chancellor of Leeds Metropolitan University, Simon Lee, was resigning following allegations about his treatment of staff, which he denied. Other vice-chancellors have also announced that they are to leave early, before the end of their terms.

One is Professor Stephen Hill, principal of Royal Holloway, University of London, for the past seven years, who is taking a sabbatical until his retirement in 2011; the other is Professor Bill Macmillan, vice-chancellor of the University of East Anglia, who had been in post for two-and-a-half years when it was announced, out of the blue, earlier this year that he was taking early retirement.

These departures are leading to worries that governing boards – increasingly made up of businessmen and women rather than academics – are running the show, and that it might not always be in the best interests of the universities and the wider public. The University and College Union is concerned, particularly about the secrecy surrounding the recent departures, and experts are worried about the possible constitutional implications.

"What's happening is quite dangerous," says Roger Brown, former vice-chancellor of Southampton Solent University and professor of higher education policy at Liverpool Hope University. "The vice-chancellors are the professionals and the governors are the amateurs. You can't have a bunch of amateurs running a university."

It is also a matter of concern for Robin Middlehurst, professor of higher education at Kingston University, although she emphasises that the direct cause for each departure may not always have been the same. "Good governance is about strong relationships and a shared understanding between people," she says. "The key is, first, the relationship between the vice-chancellor and the clerk to the council, as well as the governors. And it extends to the senior management team collectively.

"In the end, it's about good relationships between the vice-chancellor and chairman of governors because they have a very particular job to do."

Ewart Wooldridge, chief executive of the Leadership Foundation for Higher Education, agrees. "We must be careful not to see a trend here," he says. "There are a number of factors that make that relationship intense, and very likely that there are going to be tensions."

For more than 20 years – ever since the Jarratt Report in 1985 – there has been a shift in the balance of power between governing boards and vice-chancellors. Today the governors have unambiguous responsibility for the health of a university. This strengthening in their power has been driven through by a little-known body called the Committee of University Chairs (CUC), which has produced guides, a code of practice and performance indicators against which governors can judge their institution.

These publications make clear that governors are "unambiguously" responsible for the employment of staff and for overseeing the institution's activities, including its strategy. Crucially, the Higher Education Funding Council has supported all this, even though technically it has no standing in such matters.

At the same time there has been a move to make governing bodies smaller, which inevitably means fewer academics and more outsiders, who may have no understanding of university traditions. Tellingly, City University has a small board of only 15 members.

The beefing-up of governing bodies' powers has put vice-chancellors under increasing pressure. "The governors will ask: 'Why is our university in the bottom half of this newspaper's league table? Why are you not doing this and that?'" says one old hand. "This puts the vice-chancellor under enormous pressure. Their salary, their bonus, is dependent on it."

This is exacerbated by the tendency of universities to put vice-chancellors on fixed-term contracts of five years, with the possibility of renewal for another five. At the same time, there has been talk about professionalising governors by paying a fee, for example, to the chairman of the board. This idea is being actively debated within CUC and could reinforce the tensions.

The relationship can go wrong if the governors try to take over the institution and run it on a day-to-day basis, according to Mike Thorne, former vice-chancellor at UEL and now boss at Anglia Ruskin University. "They are then crossing the boundary of the executive functions of the vice-chancellor."

But it can also go wrong if the vc says, "Clear off, this is nothing to do with you. This is my institution," according to Thorne.

But it is only a handful of universities where the clash between the top dog and the governors has come into the open. This seems to be happening at relatively unsuccessful universities, says one expert. City came 44th out of 113 in the Complete University Guide, published in The Independent.

"The governors are looking at all the league tables and beginning to ask whether there is something wrong with their institution because it comes so low down in the league tables," says the expert.

"They're taking a much more managerial view of the vice-chancellor and a much more sceptical view of academics. If academics are not on the governing body – and they aren't in the post-92 universities – it's pretty easy to see them as a lot of troublesome employees."

Not everyone is so gloomy, however. Professor Thorne says: "I think it's a good system if it's working well with checks and balance on both sides. And it's healthy to have tension between the vice-chancellor and the chair of council."

According to Sir Andrew Cubie, former chairman of CUC, the new emphasis on where responsibility lies in universities was needed to clarify the role of the board and the purview of the vice-chancellor. "The issue is not different to what you would find in a corporation where the relationship between the two pivotal people – the chair and the chief executive – is absolutely essential to the good running of the institution," he says.

"But no matter how good the structural position, if the chemistry isn't there, if there isn't respect, that will not be to the good of the institution."