Whistleblowers at Anglia Polytechnic University have now asked the ÖйúAƬ Funding Council for England to intervene to examine their complaints.

At St Austell College, education secretary David Blunkett has said that the external report on complaints there should be made public. And at two universities, Hull and Middlesex, editors of internal newspapers are in dispute with their universities over the extent to which they can report internal debate which is uncongenial to the management or the marketing department.

Without going into any of these disputes, it is time to ask some questions about institutional governance. The problem is not that things go wrong sometimes. That will always be the case. The question is what should be done when they do.

The brush-it-under-the-carpet technique may be time-honoured and may seem the least damaging approach at the time, but it is not reliable as a way of avoiding bad publicity nor an effective way of running institutions. It breeds complacency within and worse coverage when it leaks, which with new legal protection for whistleblowers is now more likely.

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Universities and colleges are in the open debate business. Suppressing scandals, disputes or inconvenient views does more to bring such institutions into disrepute than any internal criticism - provided that criticism is dealt with openly. Suppression invites more questions about what else may be being massaged for market advantage: research results to suit sponsors: appointments to please donors: admission grades for rich overseas students: degree passes to improve league table rankings?

Universities and colleges which have not yet done so (and the recent Public Accounts Committee report suggests there are quite a number) should quickly review complaints procedures and rules for governors. It is no good vice-chancellors and college principals standing aloof from internal disputes: they need to make sure they are alerted to trouble early and get it sorted out before it festers, calling in the police if that is appropriate. Where vice-chancellors and principals are themselves involved, the responsibility falls to the chairman of council or governors, who may need to call in outside help.

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The role of governors and council members in new universities and colleges has been transformed as a result of independence from local government control. In old universities funding pressures and demands for accountability have changed the climate. Membership of governing bodies should no longer be an honour dished out to famous alumni, local bigwigs or the vice-chancellors' or principals' friends. Being a governor or council member is now a job equivalent to that of a company director - and includes, as flexibility in pay increases at the senior levels, setting senior staff remuneration. Appointments must be open and need to bring in people with management nous. Vice-chancellors should no longer regard their councils just as useful talking shops embracing a wide range of opinion but deciding little.

It is extraordinary that, according to the PAC, one in ten institutions still do not have registers of governors' interests. Equally extraordinary is the blithe dismissal of recommendations in Dearing that members should serve for limited terms and the number of governors should not exceed 25.

If the Arts Council was too large at 23, councils in the old universities, which can be well over 40, are never going to be effective decisionmaking bodies. That may be the way vice-chancellors like it, but the business of running universities is now so complicated, with multiple revenue sources, ever-increasing demands for accountability and growing litigiousness, that amateur arrangements are no longer appropriate. They simply invite government interference.