The scientist who concluded that organic food is no healthier than conventional produce has been bombarded with abusive messages from zealous environmentalists.

Dr Alan Dangour, a nutritionist at the London School of Hygiene and Tropical Medicine, told The Independent that hundreds of people had contacted him since his work was published, with many accusing him of dishonesty and incompetence in emails peppered with swear words.

"A lot of them have been unpleasant reading," said Dr Dangour, whose controversial study found no evidence that organic food was significantly healthier than food produced using chemicals. "They were saying I'm a quack [and that] I should do something else and stop wasting my time, but also a lot of stuff saying I must have been funded by Monsanto or big industry."

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The academic said that, although he was not upset by the correspondence, he was surprised by the strength of feeling on the issue. His research, funded by the Food Standards Agency, could hit the £2bn-a-year organic industry, which is already losing sales in the recession.

In another blow to its reputation yesterday, John Mackey, the boss of Whole Foods Market, criticised his US company's flagship British store in Kensington, west London, for selling too many fatty organic products. "We sell a bunch of junk," he said, admitting the need to concentrate on health at his UK division, which lost £36m last year despite the considerable public interest in organic produce.

Research shows that nine out of 10 British shoppers buys organic, but debate has long raged about whether it is healthier for shoppers as well as better for the environment.

Dr Dangour's study, published last week in The American Journal of Clinical Nutrition, has polarised opinion between those for whom it has confirmed long-held suspicions and those who believe it was one-sided. In an article in The Daily Mail the food writer Joanna Blythman, branded the study a "cancerous conspiracy".

Dr Dangour, whose team reviewed 50 years of scientific papers, estimated he had been sent between 250 and 300 emails, with hundreds more arriving at the FSA and his university. Among the more printable comments were: "Shame on you and this bogus so-called study," and: "To the quacks who wrote the study and concluded that organic foods have no health benefits over conventional foods: you blokes are freakin' whacky."

Dr Dangour, who said he found the abuse "mildly entertaining", added: "I have received an awful lot of emails. Half have been positive, saying we really needed this, and I have received a lot of negative emails, some of which have been abusive. I'm not sure I expected that. I was quite taken aback.

"Some have questioned my integrity and independence; whether I am funded by big agriculture or industry. It's professionally hurtful for people to say: 'You must be funded by industry or otherwise you wouldn't have come up with that finding'."

Organic supporters have complained that Dr Dangour's study should have looked at the impact of pesticides on health, while others pointed out that the work did not nullify the environmental benefit of organic farms, which are generally acknowledged to be good for wildlife. Others said they bought organic food because it tasted better.

The Soil Association, Britain's main organic certification body, pointed out that while all 162 relevant studies reviewed found organic to be higher in many nutrients such as beta-carotene, the review concluded there were no important benefits from only 55 "high-quality" studies.

Dr Dangour called the group unfair, saying: "They obviously have their own point of view but in certain circumstances the way they tried to make their point has not been entirely appropriate. If you pull random numbers from the report and claim that they are significant, that is not helpful."

Peter Melchett, policy director of the Soil Association, distanced the organisation from any personal attacks. But, in a sign that the public debate on the topic is unlikely to be quelled soon, he described the study as "bad science". "It is the nature of science that bad science doesn't last and I'm convinced that this is bad science," he said.

"Over the weekend, a number of scientists around the world have read the papers, and the fury that's building against the study from serious and reputable scientists is enormous."

The Soil Association has long suspected that the FSA is anti-organic, a view fuelled by criticism of the organic movement by the agency's first chairman, Sir John Krebs. Yesterday, the FSA stood by its research, describing it as "the most scientifically rigorous, independent review of research ever carried out in this particular area". "Opinion has, at times, been rather polarised," it added. "The FSA is neither pro- nor anti-organic food and recognises that people choose to eat organic for many different reasons."

One source in the organisation said that it had been surprised by the "near religious" tone of some of the criticisms of its research.

Dr Dangour insisted: "I'm not pro- or anti-organic. I'm a scientist and I pulled together a leading team of nutritionists for this research. We have done it entirely properly and correctly and it has been peer-reviewed."

He said he would have liked to have included new EU-funded research into organic nutrition by Newcastle University published in April last year – after the February cut-off date for his research period set by the FSA. Another report from the EU study, which has provisionally found that organic food is healthier, is due to be published in an academic journal later this year.

Dr Dangour said the existing evidence was robust enough to come to a judgement about the nutritional content of organic food and said the number of studies was better than for many other meta-analyses.

Professor Anthony Trewavas of Edinburgh University, an ardent critic of organic food, backed him, saying: "The trouble is that ideologues have propounded the idea that organic must be better for you simply because it's more natural. Nothing really could be further from the truth."

Conclusive proof about the differences between the two farming systems could come only from cohort studies of illnesses over a long period of time – like the 200 studies done to prove the link between diet and cancer – and these were unlikely to be funded, added the Professor Trewavas, an expert in plant biochemistry. "If you are eating the recommended diet of five portions of fruits and vegetables a day that is designed to saturate you in minerals and vitamins, there is no benefit from eating more," he said. "The fact is that the five a day from conventional farming is perfectly adequate for our health."

Nutritionists pointed out that, whatever the truth of the organic debate, Britons still ate too few portions of fruit and vegetables. Adults eat an average of 2.7 portions a day against a Government recommendation of five.

Helen Tracey, of the British Dietetic Association, said studies showed that some organic products, such as milk, were significantly higher in nutrients. "We don't always recommend organic as better," she added. "We say it is much better to have a good range of fruit and vegetables that you can afford."

Organic food: Is it worth it?

* Shoppers buy organic food for several different, sometimes overlapping reasons. Some say it is healthier on the basis that it contains extra vitamins and minerals, or because it uses fewer pesticides than other food, which can contain pesticide residies. Others feel organic is better for the environment, because organic farms do not use nitrogen fertiliser derived from petro-chemicals or they are richer in wildlife. Others say it tastes better.

* The FSA's 50-year review of scientific literature deals with only one of these reasons, albeit an important one: nutrients. The study concluded that there were no important health benefits of organic food in relation to vitamins and minerals. To the anger of some, the study did not address the controversy surrounding pesticide residues. The official Government position is that the vast majority of pesticide residues are safe for human health

* One significant drawback of the research is that its period of analysis meant that it did not take account of a four-year EU study, which has provisionally found that organic food is significantly richer in vitamins.

Organic debate: The shoppers' verdict

Frank Naba, 17, student

I eat organic food about four or five times a week. Mostly vegetables, chicken, eggs – that stuff – it's healthier. My mum has always given me organic food since I was a baby. Now, the older I get, the more organic food I want. It's healthy. It builds me up strong. Well, I thought it was healthy until recently when they said it made no difference.

Jim Rogers, 34, business and finance manager

I do eat organic food. Generally, it tends to be better quality. If you want to eat organic chicken, you have to pay the price. There's always a level of concern about how organic the food really is. But still, regardless of what they say the health benefits are, you can eat that meal and know that nothing artificial has gone into the process of making it.

Wendy Parker, 28, council worker

I try to buy organic food. Fruit and veg mostly. I try to cut down on how much meat I eat – just a couple of times a week now so I can afford the organic stuff. I think it's healthier and I think it tastes better. It's better for the farming economy and the environment as well. From what I've read previously, I certainly have the feeling organic would be better for you.

Lillie Nodar, 50, manager of a software company

The taste is different, obviously, and there are too many poisons around anyway. It's good for the earth and there are no chemicals used in the production cycle of organic food, so it's win-win. I'm not really surprised [by the FSA findings]. It's to do with perception. There's a lot of brainwashing that goes on. It's a fashionable way of doing things.

Jane Parks, 64, Retired

I don't eat organic food. There's so many arguments for and against, and there's a risk of some of it not actually being organic. Some things, frankly, don't obey trade descriptions. It's too expensive and it's pointless. It isn't any better for you. I don't think it's any worse. If you want to be precious, be vegan, but you're taking the joy out of life.

Interviews by Elliot Ross

£36m

Whole Foods losses last year.