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Athol Williams, who was supposed to help straighten out Bain after its controversial role at SA Revenue Service, publicly announced his resignation during a speech on Thursday, accusing the American consultancy of "withholding".
Bain in December apologised for the work it did with SARS, saying that in hindsight there is evidence to suggest that the tax agency's former commissioner Tom Moyane "was pursuing a personal political agenda".
The Nugent commission, which investigated SARS, found in a report that Bain had a part in a restructuring process which saw 200 senior staff members shifted without explanation, the Large Business Centre shut down and the fragmentation of tax agency's ability to collect revenue.
"The effect was devastating for many employees who were displaced, and proved to be detrimental to the efficiency and governance of SARS," the commission found.
The Bain restructuring process coincided with the revenue service experiencing a widening tax collection gap, forcing Treasury to borrow further to fund the deficit.
Williams, who is a senior lecturer specialising in corporate responsibility and ethical leadership at the University of Cape Town's Graduate School of Business, was appointed by Bain to oversee the implementation of Bain's "remedy plan" in South Africa. He previously worked for Bain in various capacities between 1996 and 2010.
Williams also submitted a report into Bain to the Nugent commission, which has not yet been made public.
On Thursday he resigned during a speech at the 2019 Finance Indaba, held at the Sandton Convention Centre.
Before he announced his resignation, he talked about the Bain report he submitted to the commission "for the first time".
"The big finding in my report was that, indeed, as Judge Nugent had concluded, not all relevant documents that Bain had access to where shared with the commission."
He believed the organisation was still "withholding", and "by my measure of full revelation, not doing what they need to do for South Africa".
The consultancy did not immediately reply to a request for comment.
Williams also blamed "the danger and pressure he was facing" for his decision.
According to remarks sent to the media, Williams told the summit that "people threatened me or refused to take my meetings, and the entire remedy plan fell flat because no one would engage with me. Public officials pointed me out as the face of corruption in corporate South Africa".
SA wasn’t being receptive to someone "going into a company [accused] of doing wrong and trying to help from the inside", he said.
Williams said it was a "sad reflection" of the state of SA society that the public appeared unable to accept that someone could return to a company accused of wrongdoing with a bona fide desire to help.
