Doctors Without Borders Executive President Jason Cone called on President Obama to support a fact-finding mission through the International Humanitarian Fact-Finding Commission after the bombing of a civilian hospital in Kunduz, Afghanistan. (Reuters)

President Obama apologized to Doctors Without Borders on Wednesday for an airstrike that killed 12 aid workers and 10 patients in Afghanistan, even as the White House withheld U.S. support for an international inquiry the relief group says is needed to investigate an attack that may qualify as a war crime.

White House press secretary Josh Earnest said that Obama had spoken by telephone with Joanne Liu, international president of the group also known as Médecins Sans Frontières, or MSF, and expressed his condolences for Saturday’s strike in northern Afghanistan.

“When we make a mistake, we are honest, own up to it and apologize,” Earnest told reporters at the White House. “The Department of Defense goes to great lengths to prevent civilian casualties, but in this case, there was a mistake, and it’s one that the United States owns up to.”

At least 22 people, including three children and 12 Doctors Without Borders staff, were killed overnight on Saturday when an American AC-130 gunship launched repeated attacks on the civilian medical facility in the city of Kunduz, where Afghan forces are battling Taliban fighters who overran the city a week ago.

Earnest said that Obama promised Liu a thorough investigation “and if necessary will implement changes to make sure tragedies like this one are less likely in the future.”

He declined to say whether the White House would support Liu’s demand for an independent investigation of the incident, but suggested the United States would back only a Pentagon probe now underway, along with separate NATO and Afghan inquiries.

MSF, which operates health facilities under difficult conditions across the globe, has insisted the U.S. military cannot conduct a reliable investigation of its own forces’ actions.

Liu, speaking earlier in the day at a news briefing in Geneva, said that an independent examination should be conducted by the International Humanitarian Fact-Finding Commission, a body that was set up in the 1990s under the Geneva Conventions.

“The facts and circumstances of this attack must be investigated independently and impartially, particularly given the inconsistencies in the U.S. and Afghan accounts of what happened over recent days,” Liu said.

Liu said the proposed commission would gather evidence from the United States, NATO and Afghanistan. After that, the charity would decide whether to seek criminal charges for loss of life and damage. The group has said the attack might be deemed a war crime.

“If we let this go, we are basically giving a blank check to any countries at war,” she said.

Army Gen. John F. Campbell clarified that the decision to provide air support to Afghan forces in Kunduz, which hit a hospital, was a U.S. decision. “We would never intentionally target a protected medical facility,” Campbell said while testifying before the Senate Armed Services Committee on Tuesday. (Associated Press)

Liu, who spoke prior to the call with Obama, noted there had been no commitments yet on official cooperation with an independent investigation.

But U.S. officials said that the United States would be unlikely to take part in an inquiry by the commission. The United States is not a party to the body.

“We do participate in some international tribunals and are party to numerous treaties, but when it comes to investigations of our military activities, we do those ourselves,” said John Bellinger III, who was the State Department’s top lawyer from 2005 to 2009.

Bellinger said the commission, which has never been activated, may not have the ability to quickly conduct an investigation of this type. “Because accidents or incidents . . . do happen not infrequently, the U.S. government knows how to conduct an investigation” such as the one now taking place.

In a statement issued later in the day, Liu acknowledged the call with Obama and reiterated her call for an independent probe to determine “what happened in Kunduz, how it happened, and why it happened.”

Obama also spoke on Wednesday with Afghan President Ashraf Ghani to express condolences for the Afghans killed on Saturday.

The president’s personal outreach is one sign of the administration’s concern about what is one of the worst instances of U.S. air power gone astray in Afghanistan in years.

On Tuesday, Defense Secretary Ashton B. Carter promised to hold those responsible accountable, if necessary. The U.S. military rarely, if ever, disciplines individual service members for “collateral damage” or other actions that occur as part of combat.

Officials are now scrambling to assemble an accurate account of what happened in Kunduz after their narrative shifted in the initial days following the attack.

While military officials initially said the airstrike took place to defend U.S. forces on the ground in Kunduz, the Pentagon later revised its account. They now say the strike came in response to a request from Afghan forces, not U.S. forces, under fire from the Taliban.

There are now about 9,800 U.S. troops on the ground as the Obama administration seeks to wind down the long war there. Most are tasked with supporting Afghan forces, who lack key capabilities in intelligence and air power, while a smaller number is dedicated to tracking down militants who threaten the United States.

For the most part, U.S. forces are not supposed to be taking part in combat operations against the Taliban, as they did in the years that followed the Sept. 11, 2001, attacks. White House officials are considering additional revisions to President Obama’s plan to bring the U.S. military footprint to 1,000 or less by the end of next year.

Gen. John F. Campbell, the head of U.S. and allied forces in Afghanistan, has ordered that all forces under his command are trained again in rules of engagement that govern operations in Afghanistan.

The Pentagon has not yet said whether Saturday’s strikes violated those rules, which permit the United States to use air power in three situations: for counterterrorism operations, in self-defense or to protect Afghan forces “in extremis.”

Ryan reported from Washington and Deane from London. Tim Craig and Sayed Salahuddin in Kabul and David Nakamura and Thomas Gibbons-Neff in Washington contributed to this report.

Read more:

The bloody history of Kunduz, from Afghanistan’s ‘Convoy of Death’ to now

In Kunduz, echoes of a 1988 guerrilla assault after the Soviets withdrew

Today's coverage from Post correspondents around the world