The 63-year-old officially retired at the end of last month after producing well over 1,000 papers assessing the evidence for the efficacy of alternative treatments.
But although his outspoken conclusion is that only about 5 per cent of such treatments are "solidly based on positive evidence", he admitted in an interview with Times Higher Education that he had started out as a "friend" of Cam.
His first job after graduating from medical school was in Germany's only homeopathic hospital, the Hospital for Natural Healing in Munich, where he was so impressed by the efficacy of some treatments that he continued to practise them "on and off" during his subsequent rise through the medical establishment.
That rise culminated with his appointment in 1990 as chair of the department of physical medicine and rehabilitation at the University of Vienna, where he had 120 people working under him. But his abiding interest in Cam convinced him to apply to become the world's first professor of complementary medicine when he saw the Exeter position advertised in 1993.
The £1.5 million to fund the position had been donated by construction magnate and Cam supporter Sir Maurice Laing. But although the philanthropist, with whom Professor Ernst became "good friends" before his death in 2008, was happy for him to subject Cam to rigorous analysis, practitioners remained opposed to his sceptical approach - despite the 700 invited lectures Professor Ernst gave on the scientific method.
"It looks to them as if we are always trying to disprove their beliefs. And in a way we are, because we are scientists. They understand alternative medicine as alternative to science, so to apply science to their field is quite upsetting for most of them," he said.
Support disappeared
His unit's growing reputation as "quackbusters" meant grants from Cam-supporting charities began to dry up. Nor were mainstream medical funders interested in funding medical trials for alternative therapies, forcing Professor Ernst to switch his emphasis to the cheaper tasks of literature reviews and disseminating information to both lay and professional audiences.
But it took two particularly upsetting incidents to convince Professor Ernst to abandon his efforts at bridge building and to make it unequivocally clear where he stood. One was the unsuccessful attempt by the British Chiropractic Association to sue science writer Simon Singh for libel over a 2008 article he wrote as part of a promotion campaign for a book on Cam that he co-wrote with Professor Ernst.
The other was the "very unpleasant" investigation to which he was subjected by the University of Exeter after he was accused by Prince Charles' private secretary of having breached a confidentiality agreement on a 2005 report into the cost-effectiveness of funding alternative treatments on the NHS. The study, by economist Christopher Smallwood, was personally commissioned by the Prince.
Professor Ernst was initially enlisted as a "collaborator" on the report, but asked for his name to be removed after a sight of the draft report convinced him that Mr Smallwood had "written the conclusions before looking at the evidence".
He was also concerned about the potential damage to public health that could occur if ministers acted on the report's claim that significant savings could be made by replacing some conventional treatments with alternative ones.
"I was boiling inside because it was complete misleading rubbish going straight to health ministers, and I couldn't do anything about it," he said.
Hence, when that draft was leaked to a Times journalist and Professor Ernst was telephoned for comment, he "did not mince" his words about its methodology - although he insisted that he did not disclose any of its contents.
After 13 months of being "treated as guilty until proven innocent", the university accepted his innocence but continued, in his view, to treat him as "persona non grata". All fundraising for his unit ceased, forcing him to use up its core funding and allow its 15 staff to drift away.
He was also given to understand that the unit would close when he retired. However, a rethink will now see him employed on a half-time basis for a further year to help recruit a successor. He hopes the successful candidate will be more "diplomatic" than he was, and will be more successful in attracting funding for clinical trials.
But he is adamant that the appointee must not "misunderstand the job as promoting alternative medicine", a failing, he believes, to which all the other professors of complementary medicine that have been appointed around the world since 1993 have succumbed.
"They present themselves as scientists but they are all using science as a drunk man uses a lamp post: for support and not for enlightenment," he said. "My unit is the only one that actually understands critical assessment as it should be."