Internal papers from the Department for the Environment, Farming and Rural Affairs (Defra) reveal for the first time the extent of the close connections between big business and scientists hired to give independent advice to Ministers. Many work as consultants for the firms, own shares in the companies or enjoy lucrative research grants from them.

Confidential documents disclose that former Environment Minister Michael Meacher and Food and Farming Minister Lord Whitty, were deeply concerned that scientists with industry links were dominating committees on everything from food safety and air quality to the imminent arrival of GM crops. Both Meacher and Whitty were alarmed that the scientists' commercial links jeopardised the independence of the advice they gave.

· A key member of the committee advising Ministers on the safety of GM products has received research funding from biotech giants Monsanto and Syngenta. Professor Phil Mullineaux also works for the John Innes Centre - the GM research centre funded by Science Minister Lord Sainsbury;

· More than three-quarters of the members of the committee which advises Ministers on food safety have direct links to major food companies and drug giants including Novartis, Astra-Zeneca and Syngenta. Its chair, Professor Ieuan Hughes, has personal interests in Pharmacia - which in April was bought by Pfizer to create the biggest drugs company in the world - and owns shares in BP Amoco where his daughter works.

· A former deputy chairman of the committee which examines the safety of pesticides, Professor Alan Boobis, received research funding from GlaxoSmithKline for his department at Imperial College but never declared it. Other members of this committee have links to agrochemical firms like Aventis, Astra Zeneca and Monsanto. The current head of the body, Professor David Coggon, was a close friend of Esso's chief medical officer and received a gift from the oil giant.

· The chair of a group examining air quality in Britain, Professor Stephen Holgate, is a consultant to drug giant Merck. His university department has received grants from Glaxo and Astra Zeneca. Others work for biotech and drug giants like Novartis and Schering-Plough.

· Almost three out of four members of the committee advising Ministers on the cancer risks of chemicals in food and other consumer products either own shares in or work for major biotech and drug corporations;

While the scientists openly declare their interests, Meacher was so exasperated by the structure of committees advising him that he personally intervened on a number of occasions in an attempt to get more environmentally friendly members on them.

Last week it emerged that Whitty was so alarmed about the industry links on the committee advising him on the safety of farming chemicals that he broke official rules and hired a toxicologist, Dr Vyvyan Howard, who is known to be more sensitive to environmental issues.

In one internal Defra document, Meacher scribbled his concerns in the margins: 'I do not agree with this. No member of the Advisory Committee on Pesticides should have current commercial considerations because this fundamentally undermines their integrity and judgement.'

Alongside his comments, a government official admits that Whitty shares his concerns and will be writing to the relevant parties to make his concerns clear.

Last night Meacher told The Observer: 'These committees are absolutely critical. They give definitive advice which Ministers at their peril seek to overturn. I constantly argued that nobody with significant commercial links should be allowed to sit on these bodies. It is vital they are truly independent.'

Tony Juniper, director of Friends of the Earth, said: 'It is now crystal clear how big business is setting the agenda right at the heart of government. The whole process needs to be opened up and made transparent. How can the public trust what Ministers say if their advice is coming from those with vested interest in the biotech or pharmaceutical industry.'

A Defra spokesman said the committees publish their members' interests.

He went on: 'Defra has full confidence in the capability of independent advisory committees across the range of issues the department deals with to provide high-quality, well-informed advice and support.'

The Observer contacted many of the Government's scientific advisers, who denied that their links to industry compromised the impartiality of their advice.

Professor Boobis, who took legal advice on which interests he should declare, summed up their view: 'It is almost inevitable that any scientists of international repute will have some current or past links with industry.