Alastair Campbell was threatening the BBC with "public controversy" over its Iraq war coverage two months before Andrew Gilligan's report accused the Government of "sexing up" the weapons dossier.
Newly released documents show that in March, Downing Street and the BBC were drawing up battle lines for the confrontation which preceded the death of Dr David Kelly.
In a letter to Richard Sambrook, the BBC's head of news, Mr Campbell warned of Tony Blair's displeasure about BBC reporting. He said: "You may be interested to know the Prime Minister has also expressed real concern about some of the reports he has seen and heard. I feel strongly that if the BBC reporting continues as it is, it will become a public controversy." Mr Sambrook replied: "I note your comment about possible public controversy over our reporting ... If you wish to make this public, so be it. We shall strongly fight our corner."
Among the 900 documents put on the internet by the Hutton inquiry on Saturday was an e-mail from Kevin Marsh, the editor of Radio 4's Today programme, which first broadcast the claim that the Government had "sexed up" the weapons dossier. He described how "deeply affected" he had been by Dr Kelly's death "as a result of a series of events that, in the end, I set in train".
The papers show that such was the worry about dissension in the intelligence services becoming public that the Defence Secretary, Geoff Hoon, became involved in plans to block officials from giving evidence to an inquiry by MPs. On 19 July, Martin Howard, deputy director of Defence Intelligence, laid out the strategy in a memorandum to Mr Hoon, with copies to John Scarlett, chairman of the Joint Intelligence Committee, and Sir David Omand, the Prime Minister's intelligence co-ordinator. Mr Howard said: "We should resist any calls from the ISC [Intelligence and Security Committee] to disclose the identity of the individuals concerned, call them as witnesses or have access to their written comments to line management." Another Ministry of Defence document, entitled Concerns Expressed By DIS Staff, reveals: "The DIS [Defence Intelligence Staff] personnel concerned suggested that language in the dossier was too strong on the continued production of chemical and biological agents."
The documents also show the distress of Dr Kelly's family at what they saw as a systematic campaign of denigration against him by the Government. Lawyers for his wife and daughters wrote to the Treasury Solicitor accusing Downing Street of hypocrisy, and asking why he was being subjected to anonymous smears before and after his death.
After Dr Kelly's apparent suicide, Mr Blair called for "restraint". The letter notes: "On the one hand, the Government for every good reason is calling for restraint ... on the other hand the various arms of government appear at least through the press to be following a different course."
The Labour MP Fabian Hamilton, a Foreign Affairs Committee member who opposed the war in Iraq, said last night that the Government had not amended intelligence, but "I suspect that there may have to be a sacrificial lamb. It may be Geoff Hoon."