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Lt Gen John Sattler said a group of marines was ambushed during house-clearing operations and returned fire, killing three insurgents.
Meanwhile, Iraqi troops in Falluja are reported to have found a laboratory with explosives materials and instructions for making anthrax.
Iraq's interim security minister said 2,000 people had been killed in the US-led offensive in the city.
Kassim Daoud also said 1,600 people had been detained in the operation.