Last week research commissioned by the Food Standards Agency (FSA) confirmed what was already a virtual certainty - that the cocktails of artificial additives used in many non-organic processed foods are a threat to children. Given the history of this study, the FSA's bizarre reaction left many of us dumbfounded. As the Guardian reported, scientists have been saying that additives are a threat to children and a cause of hyper-activity for more than 30 years. In 2000 a study on the Isle of Wight confirmed the risk from additives. The FSA's advisers, the Committee on Toxicity, said the study wasn't good enough to be conclusive. All of us opposed to the use of these additives responded by telling the FSA that they should commission a study that they were happy would provide a "definitive" answer.

After years of delay they did so. In the meantime, research by Professor Vyvyan Howard, sponsored by the organic baby food company Organix, and published last year, highlighted the danger of particular cocktails of additives. Then last week the Southampton study did indeed confirm the conclusions of the Isle of Wight study. What came as a surprise was that the FSA, having commissioned a study to give them a "definitive" answer, had the barefaced cheek to announce that the results were not definitive. They were. The lead researcher, Professor Jim Stevenson, said it provided clear evidence that children who consume a mix of additives can suffer changes of behaviour and that this could affect children in the whole population.

These artificial additives should be banned from all food. Organic food manufacturers produce good quality, wholesome food using around 40 natural additives (such as salt, sugar and baking soda) compared to over 400 additives, almost all artificial chemicals, used in non-organic food. The fact that these artificial additives, preservatives and colourings, are a threat to children's health is also a threat to the multi-billion pound food-manufacturing industry. They depend on these additives to give colour and taste to the cheap, mass-produced ingredients they use, and to give their products the long shelf life that global distribution systems require. But this does not excuse the FSA abandoning its principles of openness and impartiality, as it appears to have done when it received Professor Stevenson's report.

The FSA has admitted they had a secret meeting with the food industry before the research was published. As far as I can tell, no independent public interest groups were involved in these discussions. The FSA's reaction when they find scientific evidence that ingredients in processed food are harmful to health, as with salt, sugar and fat, has been to insist on new, clear labelling, for example with a traffic-light scheme. In the face of scientific evidence of harm from additives, the FSA have told worried parents to look at the ingredients list. They have already said that harassed shoppers can't be expected to spot salt, sugar and fat in such lists, so how on earth can we be expected to remember which of the 400 additives are particularly dangerous, whether it's E102, E122, E211 or E110? Worse, we need to be briefed on both the common and scientific names of these additives, and their American names, as all of these can appear on labels in British supermarkets.

The creation of the FSA was one of those early reforms of Tony Blair's New Labour government originally intended to mark a radical change from the past. Gone would be the days when food safety played second fiddle to the interests of big food companies and industrial agriculture. Secrecy, private commercial lobbying and the unethical combining of political policy on food and regulation of food safety in one department, would be swept away. The FSA does score high marks for public trust, it has stood up to the food industry over excessive salt, sugar and fat in processed food, and clamped down hard when illegal additives like Sudan I were found in processed food. It holds its board meetings in public, in general consults widely, and usually takes great trouble to talk to a wide range of interests before reaching decisions.

Two years ago, the FSA asked Baroness Dean to conduct an independent review of their operations, and her report confirmed this positive assessment - with just two qualifications. Lady Dean said that in two areas - GM and organic - the FSA was seen by many of those she consulted as having departed from its objective of relying on scientific evidence. The FSA were widely regarded as pro-GM and anti-organic. Given the strong personal views on these issues of the FSA's first chairman, Sir John Krebs, which he insisted on bringing to his work at the FSA, the reputation was well deserved. Lady Dean's report apparently had a significant impact on the FSA's board, clearly annoyed that their good work had been undermined by Krebs' personal crusade.

The appointment of Dame Deirdre Hutton to replace John Krebs was widely welcomed as an opportunity for the FSA to clean up its act in these two areas. Significant staffing changes at senior levels in the FSA followed. The agency, formed in large part from the old Ministry of Agriculture, Fisheries and Food (MAFF), had been dominated by a number of old MAFF staff who carried the pro-agribusiness attitudes of that department with them to the FSA. In some meetings with FSA officials you could sit and watch younger staff react with open-mouthed (but silent) horror at the bias being displayed by their bosses. Since Deirdre Hutton's appointment, the FSA has adopted a far more neutral attitude to organic food, but it seems that there are still areas where the Krebs and old MAFF legacy persists. The Committee on Toxicity, which advises the FSA on additives, has a long and distinguished record of being completely wrong on the cocktail effect of both pesticides and additives, and the advice it gives seems designed to try and salvage its own reputation in the face of growing evidence that its critics are right, and have been for decades.

GM is another area where the FSA is still getting it horribly wrong. Last year, illegal GM rice, not cleared for human consumption anywhere in the world, turned up in US long-grain rice imports to the UK. As a subsequent court case brought by Friends of the Earth revealed, the FSA miserably failed to meet their legal obligations to protect the public. Ignoring the fact that this GM rice was illegal and that there was no evidence it was safe to eat, the FSA originally told supermarkets they didn't need to bother removing it from their shelves. FoE's successful campaign forced a series of changes in the FSA's position, all endorsed by the judge who eventually heard the case. But delay, prevarication, lack of concern for the public interest in the face of GM corporate interests, and secrecy characterised the FSA's behaviour throughout.

When it comes to GM, the FSA seems to have learned nothing. They are now carrying out a review of their response to the illegal GM rice, which they promised during the legal proceedings brought by FoE. But even the FSA's review is both slow and secretive, excluding all but a few interested parties. If Lady Dean were to conduct another review of the FSA's performance today, it is hard to see her coming to a different conclusion on GM, with the FSA in conflict not only with scientific evidence but now also with the law.

The FSA's chair, Deirdre Hutton and her board, have done a good job in putting right some of the problems bequeathed to them by John Krebs and identified so clearly by Lady Dean. But there are areas where things seem to be getting worse rather than better. The government, at least until Tony Blair left office, was one of the most pro-GM in the world, but the agency is meant to be independent, not Blair or Krebs' genetically-engineered poodle. MAFF's successor, the Department of the Environment, Food and Rural Affairs, is still in awe of the big food multinationals, and there is a whole generation of scientists even more committed to industrial food production than the government. The FSA has to break free from these scientists' refusal to admit their past mistakes. The Food Standards Agency is in danger of becoming a double-standards agency when it comes to GM and the key building blocks of industrial, processed food - pesticides and additives. The public deserve better.