KABUL, Afghanistan — For the second time in less than a week, President Hamid Karzai of Afghanistan has picked a high-profile fight with his American allies, in the midst of a grand council that he convened to support a long-term security agreement with the United States.

American officials reacted with anger and exasperation on Saturday after Mr. Karzai publicly accused American Special Forces troops of killing civilians in a raid on an Afghan home; American officials said it was an Afghan-led raid that killed only insurgents.

Moreover, Mr. Karzai’s aides continued to insist that even if the council, or loya jirga, ratified the bilateral security agreement with the United States, Mr. Karzai would not sign it until next year, after a presidential election to choose his successor, but before he leaves office.

The remarks from the president’s camp left many people wondering why Mr. Karzai had convened a loya jirga, bringing to Kabul 2,500 Afghan notables from around the country, dismissing most employees from work for six days and locking down a city of five million so thoroughly that all roads to it were blocked for several days.