Local officials said the strike was aimed at Taliban fighters and missed, hitting two family homes.

But in a conflicting account, a high-level NATO official said Sunday night that nine civilians were killed in the strike, which was aimed at five insurgents who attacked a coalition foot patrol and killed a Marine. The insurgents continued to fire from inside a compound when NATO forces called in the strike.

“Unfortunately, the compound the insurgents purposefully occupied was later discovered to house innocent civilians,” the official, Maj. Gen. John Toolan, commander of NATO forces in the Southwest region, said in a statement. The general apologized for the civilian deaths on behalf of all coalition forces, including Gen. David H. Petraeus, the top coalition commander in Afghanistan, and said the investigation into the episode was continuing.

“While I know there is no price on human life, we will ensure that we make amends with the families in accordance with Afghan culture,” he said.

Civilian deaths have strained relations for years between the NATO-led military coalition and the Afghan government, and NATO has made efforts to reduce them.

President Hamid Karzai, who has frequently condemned NATO for civilian casualties, called the deaths in Helmand “shocking” and said in a statement that “NATO and American forces have been warned repeatedly that their arbitrary and improper operations are the causes of killing of innocent people.”

Witnesses said that an unknown number of bombs fell about 11 p.m. Saturday, landing on two family compounds in the Salaam Bazaar area of Now Zad District, a small farming community about 50 miles north of Lashkar Gah, the capital of Helmand Province.

Five girls, seven boys and two women were killed as they slept, the provincial governor’s office said in a statement. An additional six people were wounded. President Karzai later said the dead included 10 children, two women and two men. The conflicting accounts reflect a day of chaos and confusion as local government and NATO officials tried to investigate the episode.

Grieving friends and relatives drove through the night transporting eight bodies to the provincial hospital in Lashkar Gah, a resident of the village, Haji Janan, said. The other bodies remained buried under rubble as villagers tried to dig them out, he said.

The governor’s office released photographs of men carrying the dusty, bruised bodies of dead children swaddled in sheets into the hospital.

“We brought the dead bodies to show it to the officials, to show that the dead are innocent civilians, not the Taliban,” Mr. Janan said.

NATO was also investigating an air assault last week in Nuristan Province that drove out Taliban fighters after they had overrun part of a district center. A joint force of NATO soldiers and Afghan commandos called in airstrikes on Wednesday when they came under fire in the district center of Do Ab. The airstrikes drove hundreds of insurgents out of the town and killed more than 10 of them, NATO said then.

But provincial officials now say that NATO helicopters also killed more than 20 police officers dressed in civilian clothes. Qazi Anayatullah, head of the provincial council, said that as coalition forces arrived, the Taliban fled, leaving their flags flying over police checkpoints they had overrun. When the officers in civilian clothes re-entered the checkpoints, the Taliban flags were still flying, and NATO helicopters bombed them, he said.

“They mistakenly thought they were Taliban because the police were wearing local dress,” Mr. Anayatullah said. Another local official said the police officers had changed into civilian clothes after the initial Taliban assault, hoping to avoid capture.

Lt. Tyler Balzer, a spokesman for the NATO-led military coalition, said a NATO assessment team had been in Do Ab for several days. “We’re hoping a clearer picture will come out soon and we’ll be able to release the findings,” he said.

But the episode points to the murky nature of the war and the difficulty of distinguishing between Taliban fighters and armed officers or civilians dressed in traditional garb.

General Petraeus issued a reminder to his forces recently about “the need to balance tactical aggressiveness with tactical patience.”

“Every loss of innocent civilian life is a tragedy for the family involved and diminishes our cause,” he said in a May 15 memo.

The latest episode came at an emotionally turbulent time. As images of the children killed in the Salaam Bazaar attack were broadcast on television Sunday, the nation was still reeling from a suicide attack a day earlier at the governor’s compound in the northern province of Takhar. The attack killed six, including the region’s senior police commander, Gen. Daoud Daoud, a revered figure in the region from his days as an anti-Taliban fighter.

His death complicates transition efforts as NATO forces begin transferring security responsibilities to Afghan forces in seven areas of the country this July. One of those areas is Mazar-i-Sharif, where General Daoud was based.

In a statement on Sunday, the United States Embassy in Kabul said General Daoud “was in the forefront of his country’s efforts to defeat the insurgents and bring peace and stability to Afghanistan.”

His death could bolster opposition among northern leaders to President Karzai’s fledgling efforts to strike a peace deal with the Taliban.

Sensitive to that concern, the president’s spokesman, Waheed Omar, blamed foreign fighters for planning and carrying out the string of attacks that have jolted the country in recent months, trying to deflect blame from Afghan Taliban, although the Taliban have claimed responsibility for most of the attacks.

“No one from Afghanistan carries out such attacks,” he said. “All evidence shows these operations are planned outside Afghanistan and led from outside Afghanistan.”