Speaking to reporters at Camp Eggers in Kabul, McKiernan said Taliban extremists beheaded three villagers over the weekend in the start of what he described as an extended battle that ended with U.S. airstrikes killing at least 25 Taliban militants.
McKiernan noted the claims of local officials that civilians were also killed.
The international Red Cross confirmed Wednesday that dozens of civilians, including women and children, were among the dead across two villages. The U.S. is conducting a joint investigation of the incident with Afghani authorities, but McKiernan said allegations that the military was chiefly responsible for the deaths is premature.
"We have some other information that leads us to distinctly different conclusions about the cause of those civilian casualties," he said Wednesday. ()
McKiernan wouldn't reveal any of the information, saying that he preferred to wait until he could confirm the facts. He said a joint U.S.-Afghan investigation of the incident, which began Wednesday, would probably take a few more days.
"We do have people out there on the ground who will continue to follow this up with our Afghanistan counterparts to get to the truth," McKiernan said. He added: "It is certainly a technique of the Taliban and other insurgent groups to claim civilian casualties at every event, so we've just got to do the right investigation on this."
The general's remarks come as Secretary of State Hillary Rodham Clinton said the Obama administration "deeply, deeply" regrets the loss of innocent life apparently as the result of a U.S. bombing in Afghanistan and will undertake a full review of the incident.
Opening a meeting with the presidents of Afghanistan and Pakistan at the U.S. State Department in Washington, Clinton said Wednesday that any loss of innocent life was "particularly painful."
Afghan President Hamid Karzai, in Washington for his first meeting with President Barack Obama, thanked Clinton for "showing concern and regret" and said he hoped the countries "can work together to completely reduce civilian casualties in the struggle against terrorism."
Karzai will raise the issue of civilian deaths with Mr. Obama, a statement from Karzai's office said.
The first images from the bombings in Farah province emerged Wednesday. Photos from the site obtained by The Associated Press showed villagers burying the dead in about a dozen fresh graves, while others dug through the rubble of demolished mud-brick homes.
The international Red Cross team in Farah Province's Bala Baluk district on Tuesday saw "dozens of bodies in each of the two locations that we went to," said spokeswoman Jessica Barry.
"There were bodies, there were graves, and there were people burying bodies when we were there," she said. "We do confirm women and children. There were women and children."
Civilian deaths have caused increasing friction between the Afghan and U.S. governments, and Karzai has long pleaded with American officials to reduce civilian casualties in their operations. U.S. and NATO officials accuse the Taliban militants of fighting from within civilian homes, thus putting them in danger.
Mohammad Nieem Qadderdan, a former district chief of Bala Buluk, said between 100 and 120 people were killed in the attacks. He said villagers were still uncovering bodies, some of which were missing limbs or were torn into small pieces, he said.
"People are still looking through the rubble," Qadderdan said. "We need more people to help us. Many families left the villages, fearing other strikes."
Provincial authorities have told villagers not to bury the bodies, but instead to line them up for the officials conducting the investigation to see, Qadderdan said.
The fighting broke out Monday soon after Taliban fighters - including Taliban from Pakistan and Iran - massed in Farah province in western Afghanistan, said Belqis Roshan, a member of Farah's provincial council. The provincial police chief, Abdul Ghafar, said 25 militants and three police officers died in that battle near the village of Ganjabad in Bala Baluk district, a Taliban-controlled area near the border with Iran.
Villagers told Afghan officials they put children, women, and elderly men in several housing compounds in the village of Gerani - about 3 miles to the east - to keep them safe. But villagers said fighter aircraft later targeted those compounds, killing a majority of those inside, according to Roshan and other officials.
A Western official in Kabul said Marine special operations forces - which fall under the U.S. coalition - called in the airstrikes. The official asked not to be identified because he wasn't authorized to release the information.
Villagers brought about 30 bodies, including women and children, to Farah city to show the governor Tuesday, said Abdul Basir Khan, a member of the provincial council.
Journalists and human rights workers can rarely visit remote battle sites to verify claims of civilian casualties. U.S. officials say Taliban militants sometimes force villagers to lie and say civilians have died in coalition strikes. But the international Red Cross report and other official accounts added weight to villagers' claims in Bala Baluk.
In remarks in the United States on Tuesday, Karzai alluded to the problem of civilian casualties without mentioning the bombing deaths. He said the success of the new U.S. war strategy depends on "making sure absolutely that Afghans don't suffer - that Afghan civilians are protected."
"This war against terrorism will succeed only if we fight it from a higher platform of morality," he said in a speech at the Brookings Institution in Washington. Asked later to clarify, Karzai said, "We must be conducting this war as better human beings," and recognize that "force won't buy you obedience."
An Afghan government commission previously found that an August 2008 operation by U.S. forces killed 90 civilians in Azizabad, a finding backed by the U.N. The U.S. originally said no civilians died; a high-level investigation later concluded 33 civilians were killed.
After the Azizabad killings, McKiernan announced a directive last September meant to reduce such deaths. He ordered commanders to consider breaking away from a firefight in populated areas rather than pursue militants into villages.