Contrary to the belief of some in the scientific community, Dr Arpad Pusztai does not have horns or a malevolent cackle. Nor does he inhabit an imposing gothic mansion bought with the proceeds of guest appearances as an eco-hero. In fact, he lives in a modest semi in Aberdeen.

This elderly man is one of the most divisive figures in biology. Many blame him for tilting the balance in the PR battle over GM food towards public rejection. His research on GM potatoes - which came explosively into the public spotlight in a World in Action programme in August 1998 - has been dismissed as poorly done, muddled and even fabricated. Yet to anti-GM campaigners he is a hero - the scientist who stood up to the establishment and, as a result, had his career squashed at the behest of shadowy forces in the GM industry and the government.

"I think it did a lot of damage because ... the vast majority of people were somewhat neutral at the time," said Professor Chris Leaver, a plant scientist and strong supporter of GM at Oxford University. "I think the NGOs ... decided that they would make a play using him. I think he got hijacked and then he got out of his depth."

The affair finished off Pusztai's research career (although at the time he was already 69) and affected his health. His supporters were appalled by his treatment at the hands of the publicly funded Rowett Research Institute in Aberdeen, which he had served with distinction for most of his career. He was regarded as a world expert on plant lectins - defensive proteins that kill insects and other invaders - with over 300 scientific papers, including two in the prestigious journal Nature.

"I would have characterised [his treatment] as disgraceful. I don't see how any reputable scientist ... could be treated in this way," said Dr Stanley Ewen, a pathologist who was then at the University of Aberdeen and who worked with Pusztai.

Having said of GM food in 1998: "If I had the choice I would certainly not eat it", and that "I find it's very unfair to use our fellow citizens as guinea pigs", it's easy to imagine Pusztai was ideologically opposed to GM. But this is far from the truth, he tells me. "I'm strictly science-based ... It is not an ideology for me." Still, he confesses that his opposition to the technology has hardened over the years, and he still won't eat it. "Even now, I am not a campaigner. I have never belonged to any organisation campaigning for or against it."

He felt he had a duty to speak out, "just to inject some caution into this business", he says. "Make no mistake, this is an irreversible technology. It is no good 50 years later to say: 'We should have known.'"

Concerns aired

Pusztai clearly wanted his concerns to be aired publicly, but he does not come across as a man who relished or courted publicity. He was very happy, for example, that the institute's director, Philip James, shielded him from interview requests. "I was quite happy with this ... I am an academic scientist. I've never been exposed to this," he says, "I'm really not a very media person."

Pusztai says James, on the other hand, was anxious to exploit the media attention. "The director kept running around like a blue-arsed fly. This was a tremendous public relations business for him."

James even put in a complimentary phone call to Pusztai that August evening. "I telephoned Pusztai immediately after the broadcast to congratulate him on the modest way in which he had presented the evidence on the programme," says James, although he denies relishing the publicity. He says he had grave doubts about the interview going ahead in the first place.

By this stage, Pusztai was feeling extremely uncomfortable about what he was hearing on news bulletins about his own research. "I heard things that really disturbed me," he says. "My head was buzzing ... the whole thing was getting totally out of hand."

The results that Pusztai had hinted at in his interview were a comparison of rats fed ordinary potatoes and potatoes that had been genetically modified with a lectin from snowdrops. The rats on the GM diet grew less well and had immune problems even though the lectin itself caused no adverse effects at high concentrations. His conclusion was that the GM process had somehow made the potatoes less nutritious. The GM potatoes were not a commercial variety and were never intended for human consumption, but the lectin modification - which made them poisonous to insects - was an experimental model for other GM varieties.

But newspaper stories generated confusion over the nature of the genetic modification. These articles refer to potatoes modified with a lectin gene from jackbean that is poisonous to mammals. But no one can agree on where this came from. The misinformation was formalised in a press release issued by the Rowett. James says Pusztai approved it. Pusztai says he was not aware of it until it was published. Either way, the jackbean experiments that never were have proved extremely damaging to Pusztai. Even now, GM scientists dismiss Pusztai's work on the grounds of a supposed schoolboy error: of course the rats suffered, they say, they were being fed potatoes that were genetically modified to produce a poison.

The day after the World in Action programme, Pusztai's boss changed his mood from congratulation to condemnation. "My change in attitude was dramatic because I discovered that Pusztai ... had never conducted the studies which he had claimed," says James, an accusation that Pusztai strongly denies. He says he never claimed to have done the jackbean experiments. "He just simply wanted to put a real cap on it," says Pusztai. "The simplest way to do it was to suspend all research activities into this business." Pusztai's supporters claim that James came under pressure from Downing Street to put a lid on the affair.

Suspended and silenced

James suspended Pusztai and used misconduct procedures to seize his data. Pusztai's rolling annual contract was not renewed and he was banned from speaking publicly. Pusztai says he wanted to publish his results but was concerned that James would veto any approach to an academic journal.

In 1998, if James had hoped that gagging Pusztai would make the affair go away he was wrong. Continued media speculation was doing considerable damage to public confidence in GM food and this prompted the Royal Society - the UK's premier scientific academy - to enter the fray.

Although none of Pusztai's results had yet been published, it set about reviewing the information that did exist - an internal report written by Pusztai, an audit of the data produced by the Rowett, and an independent statistical analysis carried out by Biomathematics and Statistics Scotland. The data was sent to six anonymous reviewers. The subsequent report savaged Pusztai's results, but he remains defiant.

The Royal Society putdown was predictable. The reviewers had placed a hotchpotch of lab reports and statistical analyses that were never intended for publication under intense scrutiny. "There was practically nothing in it but numbers," says Pusztai. He and Ewen point out that peer reviewers had praised the methodological details of the experiment when their application for a £1.6m research grant from the Scottish Office was given the go-ahead.

Some of the disputed data did eventually see the light of day in October 1999, when Ewen and Puztai published a paper in the prestigious medical journal the Lancet. Because of its controversial nature, the data paper was seen by six reviewers - three times the usual number. Five gave it the green light. The paper - which used data held by Ewen and so was not subject to veto by James - showed that rats fed on potatoes genetically modified with the snowdrop lectin had unusual changes to their gut tissue compared with rats fed on normal potatoes. It has been criticised on the grounds that the unmodified potatoes were not a fair control diet.

I put it to Pusztai that he is demanding a level of testing for GM food that is not applied to conventional plant breeding. Radiation and mutation-causing chemicals, for example, are standard techniques used to create new varieties, and both can create unexpected genetic changes. He bats this away. "Two negatives don't make a positive," he responds. "It doesn't mean that I agree with those techniques."

The difference with GM, he says, is that there is a political agenda at work. "Ninety-five per cent of GM is coming from America, so naturally it is in their interests to push it," he says, "I have no ideological grounds against Monsanto [the biotechnology company]. For me it's a scientific argument. They have not done a proper job [of testing], and they are just using their political and economic muscle to foist it on us."

Does he regret speaking publicly about his research prior to publication - generally regarded as a cardinal sin by scientists? "No," he says. "I was publicly funded and I thought the public had a right to know." He also rejects the notion that he would have achieved more by waiting until the science was in print. Since he went public, he estimates he has given between 150 and 200 lectures around the world. And in 2005 he was honoured with a whistleblower award from the Federation of German Scientists.

"Even our best scientific publications - I don't think they are read by more than 50 people," he says. "This had impact ... to my damage, but it had impact."

Curriculum vitae

Born: 1930, Hungary

Job: Most recently research on plant lectins at Rowett Research Institute, Aberdeen

Before that: Postdoctoral work at Lister Institute of Preventative Medicine in London

Likes: Mozart, spicy Hungarian food, wine, British comedy

Dislikes: Mobile phones ('an intrusion into one's private life')

Married to Dr Susan Bardocz, two daughters (a lawyer and a medical psychiatrist)

· A podcast of this interview can be heard at theguardian.com/science