Edzard Ernst keeps a stack of hate mail as a souvenir. Two months after the world's first professor of complementary medicine took early retirement from his post at Exeter university after 18 years, the letters are still coming. An email from a chiropractor denouncing him landed in his inbox a few days ago, while Conservative MP Jacob Rees-Mogg tweeted earlier this week that for his latest attack on Prince Charles he should be locked up in the Tower of London.

"I've got used to it," Ernst says. "At first it was a bit depressing. At least the criticism is not racist – 'that bloody German', as it would be in France or Austria. I would find that hard to stomach but mostly I can find it amusing. It's strangely hilarious because the people who attack me are so bonkers."

This week Ernst showed how little his critics have dented his confidence. At a press conference to mark his retirement he joined in the name-calling, agreeing with a Daily Mail reporter's suggestion that the Prince of Wales is a "snake-oil salesman". In the living room of his house in Suffolk he unpacks the label with the precision on which he prides himself. "He's a man, he owns a firm that sells this stuff, and I have no qualms at all defending the notion that a tincture of dandelion and artichoke [Duchy Herbals detox remedy] doesn't do anything to detoxify your body and therefore it is a snake oil." Far from regretting the choice of words and the controversy it has generated, he appears to relish it.

For the past few years, Ernst has been on the frontline of a battle between practitioners of complementary medicine and their supporters on the one hand, and a small group of scientists and free speech campaigners on the other. "I have enemies," he says, "there's no question about it." He was the author, with journalist Simon Singh, of the book that led, via an article in the Guardian, to the latter being sued by the British Chiropractic Association for libel. The case was abandoned last year after Singh won in the court of appeal, but not before both men had spent two years defending it. It became a cause celebre.

Ernst believes the chiropractors would have targeted him if they could have, and that Singh was attacked as a result of their association. Chiropractors had been complaining about Ernst for years, particularly after he questioned the safety of spinal manipulation.

But it was a complaint from Prince Charles's principal private secretary five years ago that nearly cost Ernst his job. The letter, sent by Sir Michael Peat in his capacity as chair of the Prince's Foundation for Integrated Health, accused Ernst of violating a confidentiality agreement in relation to the publication of a report. Prince Charles denies having anything to do with the letter personally, and Ernst was cleared by a subsequent inquiry. But Ernst believes the power of the royal family has distorted public policy in relation to complementary medicine, and does not plan to let the subject drop.

Since retiring he has spent more time with his French wife in Suffolk, in their house overlooking the sea. The phone doesn't work when the computer is switched on, and there is no mobile coverage. The taxi driver who drops me there from the station says the satnav gives the postcode as an "unnamed road", and Ernst tells me with amusement that a neighbour invented the name of the lane he lives at the end of, and put it on a sign. It's tempting to view him as a man run out of town, driven into hiding, but when he tells his story, it is clear he has come out fighting. He plans to turn it into a book, "which will be interesting reading for a lot of people I think, lawyers in particular".

Ernst insists he did not set out to use his academic position to become a famous debunker. His German father and grandfather were both doctors, and like many German doctors, his father prescribed homeopathic remedies. As a teenager in Munich he was treated for hepatitis with homeopathy by a family doctor, and recovered. After he completed his medical training his first job was in a homeopathic hospital.

"The evidence 20 years ago wasn't so negative," he says. "I personally felt it might well go the other way. Of course, the assumptions on which homeopathy are based are utterly implausible, but the clinical evidence at one stage, when I started looking at this, seemed much more positive. I thought this [would be] an interesting field to investigate. Maybe there's something fundamental to discover which means it becomes plausible, if you see what I mean?"

Appointed to the new post in Exeter, he began designing clinical trials. These early days were very exciting. Ernst was pioneering a new field, and had remarkable freedom. He ran trials of spiritual healing for the treatment of chronic pain, arnica for wound healing, individualised homeopathy for asthmatic children. The results were "absolutely nil". One of the first trials was of acupuncture for smoking cessation. Again – contradicting the clinical experience of the acupuncturist who helped design the trial – the result was negative.

Didn't it get boring always finding that the answer was no?

"Of course with my background in alternative medicine I would have liked positive results, but as a scientist you have to be sure your methodology is rigorous, and that you're answering the research question as best you can."

Some results bucked the trend. A trial of a German technique used to treat eczema, involving injecting blood into muscles, was encouraging. And Ernst says the evidence – though not his own clinical research – supports some uses of acupuncture, herbal medicine, massage, hypnotherapy and relaxation techniques. Does he use any unconventional remedies himself?

"I take fish oil capsules. I've been involved in fish oil research even when I was in Munich, so I always kept an eye on what was happening in this area. In my view the data are very convincing for fish oil to reduce cardio-vascular risk, and that's why I take it."

As securing funding for trials became more difficult, Ernst's team turned to meta-analysis of other researchers' work. But he became more sceptical about the claims made for complementary treatments, and more outspoken about his doubts. When in 2005 he was asked to comment on a report on the economic benefits of complementary medicine – commissioned by Prince Charles's complementary health foundation, written by economist Christopher Smallwood and due to be delivered to government ministers – Ernst let rip.

Sir Michael Peat's letter of complaint was the result, and the investigation of his conduct which dragged on for 13 months. He remains angry about it. "There is a strain. You don't sleep well, you're edgy. Luckily my wife supported me and she said, however this ends, it's not going to be bad. They know what they're doing when they do that to you."

He was cleared, but felt he had become a persona non grata.

"Correspondence wasn't answered any more, I was put to one side, I felt ousted. I never saw the fundraiser again. Previously I'd seen him every month."

His 20 staff received letters informing them their contracts were due to end, but with incorrect dates. Ernst struggled to reassure them funding would continue until 2011, but people had lost confidence and started to leave. "The atmosphere that was created broke up the unit, then I was depressed because we had worked hard for a long time, we had established ourselves as the world-leading unit in alternative medicine research, and they were destroying it."

Why?

"I can only speculate. It coincided with that complaint."

Ernst was told the Centre for Complementary Medicine would close when the original endowment from construction magnate Sir Maurice Laing ran out. But when a new dean was appointed to head the university's medical school he agreed to take the centre under its wing, and Ernst took early retirement.

For Ernst, this is a vindication. "I feel very cheerful," he says, and he looks it. His smile lifts his whole face – now without the bushy moustache he wore for many years. He insists he didn't mind ending his career a year or two early, and he remains emeritus professor at the university.

But his feud with Prince Charles goes on. He believes there is a "conflict of interest" for Prince Charles in using his public and charitable activities to promote complementary medicine, and making money from the "Duchy Herbals" range of remedies (Ernst calls them "Dodgy Originals"). The Foundation for Integrated Health was shut last year and its finance director jailed for theft.

"I think it's an abuse of power. It's not his job to do that. He's not a politician. He's the king to be, and that is a very defined role, and it's not to mingle in health, politics or anything else.

"He would probably argue he doesn't make money from it, it all goes to good causes and so forth, but it's still preying on the gullible and vulnerable. And it implies we can all overeat and over-drink and live unhealthy lives and take a few detox tablets and everything is right again. That's not true."

Ernst points to a recent select committee report – to which he gave evidence – that concluded homeopathy is a placebo and shouldn't be funded on the NHS, and suggests that the Royal London Hospital for Integrated Medicine (which changed its name from the Royal London Homeopathic Hospital in 2007) enjoys "strong protection" from the royal family.

"Peter Fisher [the hospital's director] is the Queen's homeopath. I know him very well, we used to be almost friends, now less so … I like him as a person, he's a nice chap I think."

He suggests the royal family is the reason such reports are ignored, even as ministers struggles to make cuts and insist on evidence-based treatments in other areas. "The government looked at it and said, yeah, quite right, the evidence isn't very strong, but patient choice and blah blah blah, and therefore we continue. If that is not protection, then I don't know what it is."

Ernst's conversation is littered with public school phrases. He calls people "chaps", says his first boss at Exeter was a "true gentleman", and describes how he was threatened with a "dishonourable discharge". A naturalised British citizen, he says he and his wife like their part of Suffolk because it is as England was "30 years ago". The kitchen has an Aga, there is a dog, lots of classic country garden flowers and a view of a lighthouse.

When I ask what his wife does and he says she looks after him, I suggest he is old-fashioned. "Am I old-fashioned?" he asks her when we go to the kitchen to wait for a taxi. Yes, she says as she takes over the tea-making, and suggests this is partly because they have not had children.

So perhaps I shouldn't be surprised to see, on the mantelpiece of his study, when we go to look at hate mail on the computer, an enormous silver-framed photograph of Ernst shaking hands with the Queen. Why have you got that up there, I ask, puzzled after everything he has said. "She's a nice girl. She came to Exeter for a visit and she wanted to meet me. We had a chat and I really did like her. I'm not an anti-royalist."