On Friday, a statement posted on Karzai's website said the president "condemned in the strongest terms an operation of American soldiers that killed two innocent civilians," The New York Times reported.
"U.S. Special Forces raided a house of twin brothers in Bati Kot District on Tuesday, martyring both the brothers," the statement said.
John D. Manley, a spokesman for the American-led International Security Assistance Forces, denied any civilians were killed in the operation.
"Afghan national security forces and a coalition adviser engaged and killed two armed insurgents after being fired upon in Bati Kot District," Manley said.
Other coalition officials denied the allegations as well.
"Unfortunately some people are using allegations of civilian casualties for political purposes," an ISAF official said, speaking on condition of anonymity as a matter of official policy. "The statement goes directly to asserting this was a unilateral operation. It was not. It was Afghan-led with 100 Afghan national security force personnel and 17 coalition advisers."
"Misleading statements like this do not help in finalizing the Bilateral Security Agreement as soon as possible this year, which is essential to the future of Afghanistan and the confidence of the Afghan people," a U.S. official in Afghanistan said, also speaking on condition of anonymity as a matter of policy.