The spat arose after Alice Mahon, Labour MP for Halifax, highlighted the deaths of Iraqi children since the allied invasion.
She said: "The two market bombings killed a high number of children. If he [Hoon] wants information on the second bombing, he can go to yesterday's Independent, where they have got the number of the missile."
Fisk had collected shrapnel at the scene of a bombing on Friday where 62 Iraqis were killed in a missile attack. The shrapnel has been identified as being from a cruise missile made by US defence giant Raytheon.
Hoon responded to the anti-war MP Mahon by saying: "I would really caution Ms Mahon against relying on a particular account. First of all, the original account of the first marketplace bomb, set out in graphic detail in the Independent."
He went on to say: "What is important about this is all of us should look very sceptically at these kinds of reports, relying only on known and agreed facts."
The Independent strenuously defends Fisk on its front page, describing Hoon's comments as a "miserable attempt to brush aside unwelcome truths".
The paper wrote that Fisk was no supporter of Saddam Hussein. "Robert Fisk has a proud record of reporting what he sees. He has travelled to dangerous places and described unflinchingly what is happening.
"He prefers to speak to the people caught up in conflicts rather than report what the generals, politicians and spokesmen are saying," it said.
Fisk has previously gone from reporting the news to making the news when he was covering the invasion of Afghanistan and was set upon by a crowd and badly beaten. He refused to condemn his attackers at that time.
Hoon's comments came a day after Home Secretary David Blunkett also said that the British media was giving a distorted view of the conflict on a trip to New York. There are concerns in Whitehall that coverage in the British media is undermining public support of the war.
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