A "note of concerns expressed by Defence Intelligence Staff (DIS)", included worries about the 45-minute claim and claims that Iraq had "continued to produce" chemical and biological agents.
A letter written by Dr Brian Jones, a senior officer within the DIS, revealed that he had complained on 19 September about the misuse of intelligence in the dossier.
A letter from Martin Howard, the Deputy Chief of Defence Intelligence, to Geoff Hoon, the Defence Secretary attempted to brief Mr Hoon about DIS dissent before he gave evidence to the Intelligence and Security Committee.
Asked by Lord Hutton whether DIS concerns would have been passed on to the JIC, Mr Howard replied it was "unlikely".
Tony Blair told Parliament on 4 June, that "the allegation that the 45-minute claim provoked disquiet among the intelligence community ... is completely and totally untrue".
John Scarlett, the Joint Intelligence Committee chairman, said that he was "not at all aware of any unhappiness" within the DIS. Sir David Omand, who also sits on the JIC, said he was not aware of any dissent.
Questions arising and to whom
Mr Blair: Why did you not check with the DIS whether there was any "disquiet?"
Mr Howard: Why did you say that Dr Jones need not take "any further action" to correct the public record?
Mr West and Mr Cragg: Why didn't you pass on Dr Jones' concerns?
Air Marshal Joe French, then Chief of Defence Intelligence: Were you told of the dissent?
From his first letter to his employers on 30 June, Dr Kelly made clear that he did not recognise the 45-minute claim. He said he told the BBC journalist Andrew Gilligan the claim had been included "probably for impact".
The original JIC draft of 5 Septemberstated: "Intelligence also indicates that from forward-deployed storage sites, chemical and biological munitions could be with military units and ready for firing within 45 minutes".
When this appeared in the final dossier, however, the word "indicates" was dropped. The dossier's executive summary said that some of Iraq's "weapons are deployable within 45 minutes".
An e-mail from Mr Scarlett shows that he did take on board suggestions for changes from Alastair Campbell on the 45-minute claim. "Your proposal to replace 'could' by 'capable of being used' has been incorporated," he wrote.
Dr Brian Jones made clear he expressed "unease" and "unhappiness" at the claim.
Mr Campbell said that he had no "input, output, influence" over the claim, yet his memos show his suggestions were adopted.
Mr Campbell: Why did you deny you had "input" in the document? Why did you allow the media to believe that WMD could be launched against the West? Mr Blair: Why did you insist that Saddam posed a "current threat"?
An e-mail from Mr Campbell to Mr Scarlett states that Mr Blair was "worried about the way you have expressed the nuclear issue". It asks, "can we not go back to 'radiological device' in months, nuclear bomb in 1-2 years with help ... ?" Mr Scarlett did adopt the 1-2 years suggestion.
Later drafts cut out a section of Mr Blair's foreword that admitted "the case I make is not that Saddam could launch a nuclear attack on London ..."
An early draft of the dossier shed fresh light on the claim, proved to be false, that Saddam got uranium from Niger.
Jack Straw revealed the CIA complained the Niger allegation was "not credible". Mr Blair and Mr Campbell claimed they did not try to influence the document's content.
Mr Scarlett: Why did you insist on keeping in the reference to Niger?
Mr Campbell: Was your attempt to state that Iraq could have nuclear bombs a crude ploy to scare the public into backing war?
Naming of Kelly
A memo from Colin Smith, an official at the Foreign Office, stated "Kelly is apparently feeling the pressure and does not appear to be handling it well". A memo written by Mr Scarlett revealed that he had discussed with Mr Blair whether Dr Kelly would be subjected to "wider pressure" by clues to his identity being given.
A memo from Richard Hatfield, the MoD's personnel director, to Sir Kevin Tebbit, the ministry's permanent secretary, revealed he had assured Dr Kelly that "it would not be necessary to reveal his name".
Sir Kevin told the inquiry that: "I was told he was handling it pretty well ... He was quite robust." Mr Blair told the inquiry that Dr Kelly "was someone of a certain robustness".
Mr Hatfield said he had spoken to Dr Kelly and both agreed his name would emerge. But there is a difference between his name coming out and the MoD helping it.
Mr Straw: Why was the Foreign Office's concern about Dr Kelly not passed on to the MoD?
Mr Blair: Why did you release the statement when you were unsure Dr Kelly was Mr Gilligan's source? Sir Kevin: Who told you that Dr Kelly was "handling it well"?Reuse content