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The U.S. has characterized its airstrike Saturday, which killed 12 members of the Doctors Without Borders staff as well as 10 patients, as a mistake.
Obama pledged full cooperation with the joint investigations being conducted with NATO and the Afghan government in the morning conversation with Doctor's Without Borders International President Joanne Liu.
"The President assured Dr. Liu that the Department of Defense investigation currently under way would provide a transparent, thorough and objective accounting of the facts and circumstances of the incident and, if necessary, the President would implement changes that would make tragedies like this one less likely to occur in the future," White House Press Secretary Josh Earnest told reporters.
Later Wednesday, Liu put out a statement saying that despite Obama's apology, "we reiterate our ask that the U.S. government consent to an independent investigation led by the International Humanitarian Fact-Finding Commission to establish what happened in Kunduz, how it happened, and why it happened."
After his conversation with Doctors Without Borders, Obama called Afghan President Ashraf Ghani to express his condolences for the Aghan civilians killed during the airstrike and offered his thoughts and prayers for the victims on behalf of the American people, according to a White House statement.
Civilians 'accidentally struck' in Afghan hospital bombing, U.S. commander says
The U.S. military has said that Saturday's airstrike came at the request of Afghan allies who asked for assistance after coming under fire.
The previous Afghan government was frequently critical of U.S. strikes that resulted in civilians deaths, but in this case Kabul has taken a more restrained tone.
According to the White House, on the call Obama and Ghani "reaffirmed their commitment to strengthening the partnership between the United States and Afghanistan and to continuing their dialogue about ways to deepen diplomatic, economic and security cooperation to promote a more stable and secure Afghanistan."