Clashes with "inbred elite" at the University of the Witwatersrand Shortly after his appointment as deputy vice chancellor of Wits, Makgoba announced to
The Times Higher Education Supplement that it was his intention to replace the university's "dominant eurocentrism", and called the university leadership a "small inbred elite"
Mahmood Mamdani stated that "Makogba was a victim of the 'racialised power' entrenched at Wits". In 1997, Makgoba published a book about his experiences at Wits, entitled
Mokoko – The Makgoba Affair. In it, he affirmed his commitment to the idea of an
African Renaissance and to "transforming the higher education landscape". Guy Martin, professor at the School of Government of the
University of the Western Cape, referred to the book as "a personal account of the recent process of transformation occurring at Wits." Martin noted that, while Makgoba was "justifiably proud of his considerable achievements as an African scientist", the force with which he defends his credentials in the book "leads him to sound intellectually pompous and arrogant and utterly self-centered, if not downright egocentric". This article was debated heavily in the press, and provoked a response the following week from Robert Morrell, a professor in the Faculty of Education at UKZN under Makgoba. In that article, Morrell argued that Makgoba's article could rightfully be interpreted as "bullying managerial practice". Morrell dropped the case three years later, following the death of his wife, and citing concern for his "own health and well-being".
Accusations of stifling academic freedom at UKZN The Committee for Academic Freedom in Africa issued a statement in 2006 in protest against alleged infractions of academic freedom at the University of KwaZulu-Natal under Makgoba. This partly arose from his treatment of critics, particularly those involved with the shack dwellers' movement
Abahlali baseMjondolo, of his ordering the eviction of shack dwellers living on the campus. Later that year he brought disciplinary action against one of the critics, UKZN academic Fazel Khan, for "bringing the university into disrepute", after Khan had answered questions put to him by the media after he was airbrushed out of a picture and removed from the text of an article on a film he had made that was printed in the University newsletter. Later that year
The Mercury newspaper reported that Makgoba had threatened to, at the request of the mayor of Durban, bring evidence from the National Intelligence Agency to the council and to charge academics who had been working with the shack dweller's movement Abahlali baseMjondolo with "incitement". Staff were also banned from speaking to the media during a two-week strike in February 2006. Strikers wore T-shirts that read: "We Demand Academic Freedom". In 2007, the university senate invited faculties to make submissions on academic freedom. Preparation of the faculty of science and agriculture's submission was led by Professors
Nithaya Chetty and John Van den Berg, who spoke to the press in April 2008 after Makgoba, as chairperson of the senate, blocked the submission several times, claiming that it was "self-serving and contributed nothing to the debate." Van den Berg voiced his frustrations in the press, and sent a letter to Makgoba which he also read out at a senate meeting. Although the matter had initially been resolved by
mediation, this was rejected by university lawyers, who instead required that Chetty and Van den Berg sign admission of guilt forms, which they refused to do. Professor Chetty resigned, A representative of the Freedom of Expression Institute, said of the resignation, "I think he was forced into a position where he felt he had to resign. The disciplinary process, with such expensive legal counsel, was set up so that the professors would lose." the
Congress of South African Trade Unions, the Freedom of Expression Institute and the SA Mathematical Society. South African Education minister at the time,
Naledi Pandor raised concern over the "persistent negative publicity" the situation had generated. This was in spite of "two years of repeated criticism, both locally and abroad, of its commitment to academic freedom.". ==Public stance against AIDS denialism==