The EU has the power to ban exports of foods deemed unsafe - as it did with British beef. But its authority over member states is clouded by any number of grey areas and hindered by a miasma of committees.
What Mr Prodi wants to do is to centralise the authority, creating a pro-active office that could then seek to win new powers from member states. He also wants the unit to have greater input in the public debate over genetically modified organisms, currently treated as an environmental - rather than a food safety - issue.
Such a re-organisation of EU food safety controls could result in the creation of a Europe-wide authority, along the lines of America's Food and Drugs Administration.
The plans were attacked yesterday by the Tory agriculture spokesman, Patrick Nicholls: "Prodi appears to be modelling this on the lines of the federal regulations in the US because he clearly believes in the United States of Europe," he said.
The plans also appeared to catch by surprise Nick Brown, the Minister of Agriculture, although he has worked closely with European ministers to get the beef ban lifted.
Mr Brown said he was not aware of the Prodi plans, which could challenge the authority of Britain's independent food standards agency, being set up by the Government in the aftermath of the BSE scandal. "I have not seen any proposal for a European-wide standards agency and it would need to be considered very carefully before responding." he said. "In any event, the UK Government is pressing ahead with our own independent food standards agency to protect the public in the UK."
In a response to mad cow disease, the dioxin poisoning scare and anxieties over genetically modified crops, Mr Prodi believes it is vital to reassure the public on the safety of the food it is eating.
He has the backing of key players in his new team, including the two incoming commissioners in charge of agriculture, and consumer protection and health. Food safety issues featured prominently in discussions between Mr Prodi and the new commissioner for consumer protection and health, David Byrne, who helped to draft the legislation that set up Ireland's Food Safety Authority.
According to one senior source, that conversation convinced Mr Prodi that Mr Byrne, Ireland's former attorney general, was the "man for the job".
Mr Byrne said at the weekend: "An issue of pressing importance for the citizens of Europe will be consumer confidence in food safety. I will be looking to take measures to establish confidence and to put in place measures for rapid response to measures that may arise in the future."
Franz Fischler, the agriculture commissioner who is staying on, has publicly backed the creation of a European food safety agency, a move rejected by the last commission.
At present, the Commission's advice on food safety comes from a network of eight specialist scientific committees and one multi-disciplinary committee. Mr Prodi wants to give these teams more independence, creating a new semi- autonomous office outside the direct domain of health and consumer protection or agriculture. This could be done without incurring large-scale costs, by keeping the administrative and language translation services provided by the current Commission.
The Prodi initiative will reawaken a long-running debate in Brussels over how food safety should be handled. Those who oppose the idea of a European FDA point out that the American version has around 5,000 staff, compared with about 300 civil servants in Brussels who are devoted to the issue.