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The discovery was made at 0920 BST by a member of the police team called into search for Dr Kelly after his family reported him missing last night.
Dr Kelly has been at the centre of a row between the British Government and the BBC about the use of intelligence reports in the run up to the war against Iraq.
The row centred on a report by journalist Andrew Gilligan during the Today programme on BBC Radio Four in which he said the government had "sexed-up" its dossier on Iraq to boost public support for the war.
He accused the government of inserting a claim into the dossier that Saddam Hussein was capable of deploying weapons of mass destruction within 45 minutes
On Tuesday Dr Kelly - an expert in arms control who had worked as a weapons inspector in Iraq between 1991 and 1998 - told the Foreign Affairs select committee he had spoken to Mr Gilligan but denied he was the main source for the story.
Dr Kelly left his home in Southmoor, Abingdon, at about 1500 BST on Thursday to go for a walk. His family reported him missing at 2345 BST the same day.
The government has announced an inquiry will be held, headed by law lord Lord Hutton, to investigate the circumstances surrounding Dr Kelly's death.
The Prime Minister, Tony Blair, was on a flight to Tokyo on the first leg of a Far East tour when he was told the body had been found.
He was said to be "very distressed" for the Kelly family.
Dr Kelly has been under intense media scrutiny since the Ministry of Defence said he had come forward to say he had had a meeting with Mr Gilligan.
The MoD said Dr Kelly had at no time been threatened with dismissal or suspension for speaking to Mr Gilligan.
A spokesman said it had been made clear to Dr Kelly that he had broken civil service rules by having unauthorised contact with a journalist, but "that was the end of it".
Downing Street said Dr Kelly had been warned his name was likely to become public because he was one of only a small number of people who could have been the source.
Dr Kelly and his wife, Janice, have three daughters, Sian, 32, and twins Rachel and Ellen, 30.
Dr Kelly's body was formally identified the following day.
He had apparently committed suicide by slitting his wrist and taking an overdose of painkillers. A knife and packet of pills were found beside his body.
The BBC confirmed Dr Kelly was the main source for Andrew Gilligan's claim that the government had "sexed-up" the dossier on the case for war.
At the Hutton inquiry into his death which began on 11 August, his widow Janice said Dr Kelly had felt "totally let down and betrayed" by the Ministry of Defence.
Lord Hutton heard evidence from 74 witnesses over six weeks and viewed thousands of pages of evidence.
The report was published on 28 January 2004 and was highly critical of BBC governors for failing to investigate properly Downing Street's complaints. As a result, the BBC chairman Gavyn Davies, the corporation's Director General Greg Dyke and journalist Andrew Gilligan resigned.
Lord Hutton absolved the government of any kind of "dishonourable, underhand or duplicitous strategy" in the leaking of Dr Kelly's name to the press.
But he said the Ministry of Defence was "at fault" for failing to tell Dr Kelly that his identity as the suspected source would be confirmed to journalists who suggested it.
He said Mr Gilligan's report that the Iraq dossier was sexed up was "unfounded" and that Joint Intelligence Committee chairman John Scarlett had acted to ensure the dossier was consistent with reliable intelligence.
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