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The reports in the Washington Post and Boston Globe speak of a systematic operation in which American agents were able to listen in to secret communications between Iraqi security bodies responsible for protecting President Saddam Hussein.
The allegations come shortly after US warplanes fired on Iraqi fighter planes encroaching on a no-fly zone over the south of the country.
Quoting unnamed advisers to Mr Annan, the Washington Post report suggests UN inspectors assisted US personnel in listening to some of Baghdad's most sensitive communications.
One unidentified source was quoted by the Post as saying: "The Secretary-General has become aware of the fact that Unscom (the UN Special Commission charged with disarming Iraq) directly facilitated the creation of an intelligence collection system for the United States in violation of its mandate."
"The United Nations cannot be party to an operation to overthrow one of its member states. In the most fundamental way, that is what's wrong with the Unscom,'' the source also said.
UN neutrality 'undermined'
The newspaper said Mr Annan was "alarmed" at the implications of the evidence which, if proven, could undermine the UN's neutrality.
The BBC's Caroline Wyatt in Baghdad says if these reports are true, they will also be a vindication of what Iraq says it has known for some time.
Iraqi officials have frequently accused the weapons inspectors of spying for the US and Israel, a charge denied by the UN. It has also complained about the dominance of US and British officials on the inspection teams.
However, Terry Taylor, a former chief UN weapons inspector in Iraq, told the BBC on Wednesday he knew of no instance involving the alleged assistance.
Mr Taylor said: "To think of the UN Special Commission as a kind of system covering US intelligence and spying, I think is misguided".
Former US weapons inspector Scott Ritter says that certain information was never released.
Speaking to the Boston Globe newspaper, Mr Ritter said: "We knew a hell of a lot of information about presidential security.''
However, he said if his team found any information related to Saddam Hussein's personal safety, "we would dump it".
Annan-Butler rift
Mr Annan received the classified US intelligence about the eavesdropping activities through intermediaries, according to the Post.
It said Mr Annan had confronted Richard Butler, head of the Unscom team, with the reports of alleged help received by the US.
Quoting two unidentified sources, the newspaper said Mr Butler had denied the reports.
He was quoted by the Washington Post as saying that he had never authorised any help to member states that would serve their own purposes.
"As far as I am concerned I have always been assiduous in insisting that any assistance given to us be strictly related to our disarmament mandate," Mr Butler said.
The newspaper quoted sources as acknowledging that Mr Annan would like Mr Butler to resign in favour of someone who might be able to win the consent of Iraq and those countries on the UN Security Council sympathetic to it.
Violation of no-fly zones
Tension between allied and Iraqi military continues, following the US Operation Desert Fox in December.
On Tuesday, the first clash between Iraqi and US fighter planes since December 1992 took place after US aircraft fired six air-to-air missiles at four Iraqi planes which it said had violated no-fly zones.
The Iraqi military said that its jets had "confronted" allied aircraft that had "violated" Iraq's air space.
Following the clash, Secretary of State Madeleine Albright emphasised that the US would continue to enforce the no-fly areas, which were set up after the 1991 Gulf War.
Meanwhile on Tuesday, President Saddam Hussein made a television speech calling for all Arabs to overthrow any of their leaders supporting the US.
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The Washington Post
UNSCOM
Permanent Mission of Iraq to the UN
The Boston Globe Online
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