The University of East London's vice-chancellor resigned last week after a seven-month suspension.
Martin Everett was suspended in July 2008 by the chair of the board of governors, Jim McKenna, following allegations of a lack of leadership and vision. He resigned shortly after a report from the special committee convened to investigate the case was handed to the board.
A UEL statement says: "The board recognises Professor Everett's considerable standing as an academic and researcher, and makes no criticism of his integrity or conduct.
"However, Professor Everett and the board both believe that in the circumstances, where there has been an irretrievable mutual breakdown in trust and confidence, a new vice-chancellor would be better placed to take the university forward."
Susan Price, UEL's acting vice-chancellor, was among those whose evidence to the special committee was highly critical of Professor Everett. However, most senior academics supported him: 25 professors were among the signatories of a letter sent to the board last October demanding his reinstatement.
It is understood that the special committee's report criticised some aspects of the handling of the concerns raised about Professor Everett.
Gillian Slater, former vice-chancellor of Bournemouth University, resigned from UEL's board in June after Mr McKenna declined to give full details of the reasons for the suspension.
Staff, including staff governors, were originally told that Professor Everett was on "indefinite leave" before it emerged that Mr McKenna had offered him a payment to resign or face "procedures to remove him".
Professor Everett refused the pay-off. In a letter seen by Times Higher Education, he wrote: "These actions and proposed actions are not only unfair and unlawful, but also represent a substantial risk of the misapplication of public funds.
At Leeds Metropolitan University, Simon Lee, the vice-chancellor, was recently given an ultimatum by Ninian Watt, the chair of governors, to resign or face suspension for bullying allegations. He chose the former under a compromise agreement.
The cases have focused attention on the circumstances under which chairs may suspend vice-chancellors. Under UEL's articles of government, which are similar to those in most post-92 universities, the chair "may suspend from duty, with pay, the holder of a senior post for alleged misconduct or other good and urgent cause".
At UEL and Leeds Met, it is not clear why suspension was "urgent".
David Palfreyman, director of the Oxford Centre for Higher Education Policy Studies, said he was "astonished" by these cases.
"If you're chair in the commercial world, you can fire the chief executive officer, somebody writes a fat cheque and both of you move on, but the law of corporations is not company law. I worry that people ... don't understand the legal context in which they are operating."
He said it was unclear whether the chair of a post-92 university could offer a vice-chancellor cash to leave without prior discussion or at least subsequent board ratification.
The University and College Union branch at UEL said: "Governors are answerable to no one. They have used secretive and authoritarian methods to drive out a respected manager. We still do not know why Professor Everett was pursued in this way."