Dr Kelly, 59, had come forward and volunteered that he had met Mr Gilligan, the defence and diplomatic correspondent of Radio 4's Today programme, at the Charing Cross Hotel in central London. During an interview with Richard Hatfield, the Ministry of Defence's personnel director, the scientist was reprimanded, but told that no further disciplinary action would be taken.
But John Scarlett, the chairman of the Joint Intelligence Committee demanded that the inquiries into the scientist should not be halted but instead it should be intensified.
He wrote to Sir David Omand, Mr Blair's security coordinator at the Cabinet Office " I agree ..that the finger points at DK as Gilligan's source. Kelly need an appropriate security style interview. I think it is rather urgent."
The Prime Minister's intervention in the affair was disclosed to the Inquiry by Martin Howard, the deputy chief of Defence Intelligence who had been told carry out a further questioning of Dr Kelly.
Mr Howard recalled " high level telephone discussions between Sir David Omand and Sir Kevin Tebbit, the Permanent Under Secretary at the MoD and "possibly others" and an exchange of letters between Omand and Tebbit. He continued " I recall seeing the response from Sir David Omand to Sir Kevin Tebbit which recorded the Prime Minister's views that before we decided what are the next steps that should be taken, it would be sensible to get into a bit more detail into the differences between what Dr Kelly had and Andrew Gilligan had claimed".
The hearing heard that Sir Kevin had tried to protect Dr Kelly from public exposure appearing as a witness in the Commons Foreign Affairs Committee (FAC) inquiry into the Government's case for war.
Sir Kevin wrote to Geoff Hoon advising that he should allow Dr Kelly to appear before the Intelligence and Security Committee where the hearings are held in private, but not the Foreign Affairs Committee.
He said " The FAC have already completed their inquiry...A separate session to question Dr Kelly would attach disproportionate importance to him in relation to the subject of the FAC's inquiry as a whole ....It is fairer on the man himself not to expect him to appear before two Parliamentary Committees within two hours. The line may not be sustainable ...But I think it is worth a try at least."
However, Mr Hoon chose to ignore the advice. His private secretary, Paul Watkins, wrote in a memorandum " The Defence Secretary has...concluded that on balance we should agree to the FAC's request...I understand that No 10 would be content with this approach.
"..I am copying this letter to Jonathan Powell and Alastair Campbell( No 10) and to Sir David Omand and John Scarlett (Cabinet Office)."
In a highly unusual move, Mr Howard, the intelligence chief, was put in charge of preparing Dr Kelly for the ISC and and FAC hearings. Questioned by James Dingemans, Mr Howard denied that he was briefing the scientist for his appearance.
But Mr Dingemans produced a set of minutes for a meeting which stated " DCDI (Deputy Chief of Defence Intelligence) will brief David Kelly for the FAC and ISC and will strongly recommend that Kelly is not drawn on his account of the dossier ...Kelly is apparently feeling the pressure and appear not to be handling it well".
Whitehall officials were questioned by James Dingemans, counsel to the inquiry about why the Ministry of Defence had put out a statement alerting the media that Dr Kelly had volunteered that he was the man who had met Mr Gilligan. Mr Howard indicated to the tribunal that Mr Hoon may have had a part in this.
He said " The overall judgement reached at all levels, from ministers downwards, was that it would be necessary to make the fact that this had happened public."
In a series of hitheto unpublished documents the Inquiry saw how the final versions of the September dossier appeared to have been hardened up from previous drafts. The Inquiry also saw instruction to MoD press officers on how to respond to media inquiries about Dr Kelly, and told to confirm the name when it was put to them and play down his seniority.
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INDEPENDENT
British Parliament Foreign Affairs Committee transcript:
Evidence of Dr David Kelly
Key players in the 'sexed-up dossier' affair
Herald Feature: Iraq
Iraq links and resources