Dr Daryl Balia was employed by the university to organise the Edinburgh 2010 conference currently taking place to mark the centenary of the historic 1910 World Missionary Conference in the city.
But he complained of bullying and said "people of colour were treated as second class" by the conference, attended by more than 300 church leaders.
Hours after the university was contacted for a comment, a letter was hand-delivered to Dr Balia's home, formally suspending him from his post and warning him to make no further comment.
The letter told him he faced potential disciplinary action for "gross misconduct" by issuing statements which could be seen as "defamatory and inflammatory" and bringing the university and the Church of Scotland into disrepute.
Dr Balia, a South African Methodist minister, headed an anti-corruption programme for Nelson Mandela's government before being employed to organise the 2010 conference.
Dr Balia said he had issued the reports to make his situation clear and insisted they were not intended to be provocative.
He said there were tensions at the heart of the conference over differing attitudes to sexuality and relations with other faiths.