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Britain's former spy chief has misled the Iraq inquiry by exaggerating the reliability of crucial claims about Saddam Hussein's ability to launch weapons of mass destruction, according to the leading Ministry of Defence expert who assessed the intelligence behind the decision to go to war.

Sir John Scarlett, who was responsible for drafting the Government's controversial 2002 dossier outlining the case for invading Iraq, claimed last week that intelligence indicating Iraq possessed missiles that could be launched within 45 minutes was "reliable and authoritative". But Scarlett's evidence is contradicted by the most senior WMD analyst who saw the original intelligence. Brian Jones said that it was vague, inconclusive and unreliable.

Dr Jones, who was head of the nuclear, chemical and biological branch of the Defence Intelligence Staff in the run-up to the Iraq invasion, told The Independent that it was "absolutely clear" that the intelligence the Government relied upon was coming from untried sources. The 45-minute claim was one of the key assertions that convinced MPs to take Britain to war.

"Having said there was the intelligence to show Iraq had WMD, there was no indication in what [Scarlett] said about what is now very well known, that those additional pieces of new intelligence were all caveated," said Dr Jones. "Information was coming from untried sources – that is absolutely clear." He added that Scarlett crucially misled the inquiry about the source of the information. "The description Scarlett gave for the secondary source, who passed the information on, was 'reliable and authoritative'... If he is passing on information from someone who has never reported before then that is a nonsense."

All witnesses to the Iraq inquiry, led by Sir John Chilcot, are made to sign a written transcript of their evidence, declaring that it is "truthful, fair and accurate". Scarlett will be interviewed again next year by the inquiry team, although the current plan is to question him in private.

Scarlett was the head of the Joint Intelligence Committee when he oversaw the drafting of the September 2002 dossier. Despite the controversy, Scarlett was promoted by Tony Blair to become the head of MI6 in 2004. Although the subsequent Butler review of intelligence concluded that the dossier had been "flawed", Scarlett was awarded a knighthood by Mr Blair in 2007. He retired from MI6 earlier this year.

Dr Jones's comments will add to the pressure on Mr Blair ahead of the former prime minister's own, expected appearance before the Chilcot inquiry panel in January. Dr Jones's intervention yesterday came as the transparency of the Chilcot inquiry was challenged, when its public proceedings were censored for the first time.

Government's 45-minute claim 'very suspicious'

Dr Jones, who retired in 2003, said that the intelligence received shortly before the Government's dossier was published in September 2002 was not clear about what the 45-minute claim referred to, or the types of weapons it was suggesting could be launched in that time. In an article published on IraqDossier.com, he states that both he and a colleague concluded that the source of the intelligence was unproven, while the information itself had to be treated as "second-hand".

MI6 now concedes that some of the second-hand sources used in the dossier were unreliable. Casting further doubt on Scarlett's evidence, Dr Jones told The Independent that he was "very suspicious" about the confusing way in which the 45-minute claim was presented in the Government's dossier.

Scarlett told the inquiry last week that "there was absolutely no conscious intention to manipulate the language or obfuscate or create a misunderstanding as to what they might refer to". But Dr Jones said the dossier's assertion that Saddam could "deploy chemical or biological weapons within 45 minutes of an order to do so" did not make clear that the claim was only meant to refer to battlefield weapons, rather than those that could be launched against other countries.

And Dr Jones challenged the inquiry team to finally reveal the identity of the source that passed on the 45-minute claim to Britain's intelligence services. A senior Iraqi army officer, Lt-Col al-Dabbagh, claimed in 2003 that he was the source of the information. "If you look at what Dabbagh subsequently said, then he was talking about battlefield weapons without doubt," he said. "So then, if he was talking about battlefield weapons, did these guys deliberately avoid saying that they were? I am now very suspicious about those sorts of things."

When asked by the Chilcot inquiry whether he had been aware of Dr Jones's concerns about the claims made in the dossier, Scarlett insisted he had not been informed about them.

Iraq 'could happen again'

Dr Jones also launched a stinging attack on the Government's failure to make key reforms to the intelligence services in the wake of the Butler review, carried out in 2004 to examine the failures on Iraq. Its refusal to do so, he said, meant that the breakdown that led to the decision to invade Iraq could happen again. "As a result of previous inquiries, I don't think there's been the sort of fix that produces a permanent protection against what happened then not happening again," he said.

In particular, Dr Jones criticised the Government's failure to implement the Butler review's recommendation that more expertise exist within the JIC. "The senior representatives on the JIC from the DIS, the chief and his deputy, were both intelligence novices really compared to others on the committee," he said. "Really, in terms of intelligence, I would describe those two guys as amateurs." However, the Butler review's recommendation that the deputy head of the DIS should have a background in intelligence analysis was not accepted by the Government.

Dr Jones said that as long as institutions such as MI6, MI5, the Foreign Office and the MoD remained in charge of different areas of intelligence and the expertise in analysing it, they would continue to compete with each other for attention, rather than co-operate fully. He said only the creation of an independent body, overseeing the whole intelligence gathering and analysis process, would solve the problem.

Brian Jones: An expert ignored

Brian Jones, now retired, worked in the scientific and technical directorate of the Defence Intelligence Staff (DIS), a team of experts who analyse intelligence from MI6, MI5, GCHQ and foreign agencies for the Ministry of Defence. He was the most senior official responsible for analysing intelligence on nuclear, biological and chemical weapons.

During the Hutton inquiry into the death of the expert on Iraqi arms, Dr David Kelly, Dr Jones said he and a colleague wrote to the deputy chief of the DIS to outline their unhappiness at claims made in the Government's dossier on Iraq's weapons of mass destruction, published in September 2002. They were worried about the description of alleged stockpiles of chemical and biological weapons held by Iraq and the claimed 45-minute timeframe for launching them. He then suggested in The Independent that the whole of the DIS had concerns about the claims, but those concerns had been ignored.

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