Downing Street and ministers were forced on to the defensive as the Prince appeared to single-handedly wreck their efforts to calm fears over GM food and crops.
Just four days after Tony Blair accused the media of whipping up "hysteria" over the issue, the Prince mounted a detailed critique of claims that the biotechnology was safe.
Prince Charles is also to meet Dr Arpad Pusztai, the scientist whose research first sparked a furore over GM crops and who has since been denounced by Jack Cunningham, the minister charged with overseeing the science.
And 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 large companies involved 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 prevent Third World food shortages.
Both 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.
Mr Meacher insisted there was no intention of "forcing GM foods down people's throats" and rules governing them were "stringent and tight".
Meanwhile, Ms Ruddock's speech, to the Royal Bath and West Show in Shepton Mallet, Somerset, looks likely to open a split within Labour, where many are thought to have serious doubts on the issue.