KABUL, Afghanistan — The American military commander called President Hamid Karzai to apologize for a drone strike in southern Helmand Province, which the military conceded had killed and wounded civilians, a coalition official said on Friday.

Mr. Karzai had lashed out at his American allies after the Thursday attack, which came at a delicate moment when talks between Mr. Karzai and the United States over a long-term security agreement have reached an impasse. The Americans have told Mr. Karzai that unless he signs the agreement promptly, they will begin planning for a total withdrawal of American and NATO forces after the end of next year.

Gen. Joseph F. Dunford Jr., the American and NATO commander in Afghanistan, made a late-night phone call to President Karzai on Thursday after the president’s criticism became public. “He talked to President Karzai directly, expressed deep regrets for the incident and any civilian casualties, and promised to convene an immediate joint investigation to determine all the facts of what happened,” a coalition spokesman said, speaking on condition of anonymity in line with official policy.

Mr. Karzai vowed this week, at the conclusion of a loya jirga, or grand council, that he would cancel the security agreement completely if there was even one more raid that killed civilians.

On Thursday, he said that in effect that moment had come. “For as long as such arbitrary acts and oppression of foreign forces continue, the security agreement with the United States will not be signed,” he said.

The loya jirga overwhelmingly approved the security agreement last week and called on Mr. Karzai to sign it quickly. The Americans have said that that would be necessary to allow time to prepare for a longer-term mission.

Mr. Karzai said that he was adding a series of new conditions beyond what he had already negotiated and would not sign until those were satisfied. One of those new conditions was an immediate ban on any raids on Afghan homes. While the raids he was speaking of were primarily those carried out by Special Operations forces on the ground, his statement Thursday made it clear that he now included drone strikes in his prohibition.

The coalition spokesman confirmed that two drone incidents had taken place in Helmand Province on Thursday. The first, in Garmsir District, targeted an insurgent commander traveling on a motorcycle, but missed him and apparently hit civilians; one child was reported killed and two women were severely wounded. The targeted man fled on foot and was killed by a later drone strike. In the second incident, in Nawa Barak Sai District nearby, another drone strike killed a single insurgent target and caused no civilian casualties, the spokesman said.

“Neither of the strikes were directed at a house or hit a house,” he said. The civilian victims were apparently nearby on the road where the first attack took place. The drones were military, but in keeping with its standard practice, the coalition did not identify which country they belonged to. Both the United States and Britain are believed to have drones operating in Helmand Province.

Mr. Karzai, in a statement posted on the president’s website on Thursday night, said that a NATO drone strike on a house in Faqiran, a village in the Garmsir district, had killed at least one child and wounded two women on Thursday morning.

“This attack shows that American forces do not respect the lives and security of the people of Afghanistan and the loya jirga decision,” Mr. Karzai said. “For years, our people are being killed and their houses are being destroyed under the pretext of the war on terror.”

In a text message on Friday morning, Aimal Faizi, the president’s spokesman, said, “It makes very difficult for the president to authorize the signing of B.S.A.,” referring to the bilateral security agreement.

After Mr. Karzai announced that he wanted to reopen negotiations on the agreement, President Obama’s national security adviser, Susan E. Rice, told him in a meeting here Monday that the United States had concluded negotiations and that, unless he changed his mind, Washington would begin planning for a total withdrawal.

The bilateral security agreement provides for a 10-year American military presence in Afghanistan, beginning in 2015. Ms. Rice also said that financial aid to Afghanistan’s security forces would be imperiled without an agreement.

Both sides have continued to hammer home their positions in public statements. Mr. Karzai told Radio Free Europe, in an interview Tuesday, “If America wants to conclude a security agreement with us, America needs to respect the security of Afghan homes.”

In a public meeting in the city of Herat on Wednesday, the American ambassador, James B. Cunningham, reminded listeners that even Mr. Karzai’s handpicked loya jirga, composed of some 2,500 leaders from around the country, had urged him to sign the agreement quickly.

“Zero is not an option for us,” Mr. Cunningham said. “It could be a consequence of decisions that your government takes or doesn’t take.”

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