Within minutes the short-fused Cabinet Office minister was angrily accusing the interviewer John Humphrys of operating on a "Friends of the Earth agenda" after he had asked why the Government was not introducing a legally binding code on growing GM crops or imposing a five-year moratorium. Mr Humphrys insisted he was putting forward the view of a concerned public.
In fact, the secret document (see above) reveals the Government planned the interview as an early shot in its most vigorous campaign so far to reverse the tide of public opinion.
It shows that Friday's barrage of publicity was carefully timed to capitalise on a week which was thought to give the Government a chance to "move on to the front foot".
The document shows that a meeting on 10 May, between Dr Cunningham, the Health minister Tessa Jowell, the Environment minister Michael Meacher, and the Food Safety minister Jeff Rooker, decided that five separate planned announcements on genetic modification should be "rolled into one" to maximise the impact.
The announcements - duly presented together by Dr Cunningham on Friday to the Commons and at a press conference - heralded the setting up of two new quangos to oversee GM crops, the publication of two reports on the issue by the Government's Chief Medical Officer and Chief Scientific Adviser, and released new voluntary guidelines on growing the crops agreed with the industry.
The leaked document shows that one of ministers' main concerns was to rubbish research by Dr Arpad Puzstai, which suggested that GM potatoes harmed the health of laboratory rats. A world authority, he was forced to leave Aberdeen's prestigious Rowett Institute after be briefly mentioned the research in a television documentary.
The document says that the government announcement should be timed to follow the publication of three reports last week - by the Royal Society, the House of Commons Science and Technology Committee, and the Government's own Advisory Committee on Novel Foods and Processes - which ministers rightly anticipated would attack Dr Puzstai's work.
The document says ministers must "speak with one voice," and strongly recommends they "place heavy emphasis on the broadcast media - speaking to people directly in their front rooms". It suggests Mr Rooker kick off the day with an interview on BBC's Farming Today followed by Mr Cunningham on Today. Dr Cunningham did five other radio interviews that morning and spoke to BBC TV, ITN, Sky News, and BBC Radio's World at One directly after the press conference.
Mr Cunningham's office said it would work with Downing Street's Strategic Communication Unit "on an article - perhaps for the Sun and a broadsheet - in the name of the Prime Minister".
The document also looks at the longer-term, including making ministers available for "both popular and more specialised radio and TV programmes such as Country File, You and Yours, and the Jimmy Young Show". An instant rebuttal system was to be set up to counter reaction by "activists and other pressure groups".
The document outlines a strategy to try to get endorsement from independent bodies like English Nature, the Royal Society, the Consumers' Association and "moderate green groups". "All of these interests will not endorse the entire package - but if we are able to ensure that they do so wherever possible, this will help us to tell a good story," the document says.
In the end it did not all work out as planned, partly because the announcement had to be moved at the last minute from Thursday to Friday to stop it clashing with an initiative by Tony Blair on cancer. Many of the planned approaches to the media, and attempts to get endorsements did not take place. "The Government," said one source, "is not as well organised as we would like."