Downing Street swiftly issued a statement saying: "We don't talk about conversations that the Prime Minister has with the Royal Family."
The pair are understood to have clashed privately when they met at St James's Palace five weeks ago to discuss GM crops, particularly over ministerial efforts to denigrate anti-GM campaigners. Yesterday the Prince publicly attacked what he described as the "unethical" technology.
Downing Street and ministers were forced on to the defensive as the Prince appeared single-handedly to wreck their efforts to calm fears over GM food and crops. Four days after Mr Blair accused the media of whipping up "hysteria" over the issue, the Prince mounted a detailed critique of claims that the biotechnology was safe.
The Prince is also to meet Dr Arpad Pusztai, the scientist whose research sparked a furore over GM crops and who has been denounced by Jack Cunningham, the minister overseeing the science.
Mr Blair faces further embarrassment today. A former Labour minister, Joan Ruddock, is due to call for a five-year moratorium on the commercial release of modified crops. She believes the companies in-volved in the technology are not acting with public consent.
The Prince's intervention, in an article in yesterday's Daily Mail, warned against the "Orwellian" dangers of the science and criticised the "unprecedented and unethical" situation in which farmers' crops could be cross-pollinated with GM crops "since bees and the wind don't obey any sort of rules - voluntary or statutory".
He also ridiculed as "emotional blackmail" the Government's claim that GM techniques could help to prevent Third World food shortages.
Downing Street and Michael Meacher, an Environment minister, said they welcomed the article. "We are perfectly content for the Prince of Wales to make a contribution to a debate which, as you know, we are seeking to encourage," the Prime Minister's official spokesman said.
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