"There will be accountability as always with these incidents, if that is required," Carter told reporters travelling with him to Spain.
The situation in Kunduz is confused and complicated, so it may take some time to get the facts, he noted.
"But we will get the facts, and we will be full and transparent about sharing them with the American people, but also with the people of Afghanistan, and for that matter, the entire world, to include the essential non-profit factor, the non-governmental organisation community, which is so critical," he asserted.
"Their medical work in Afghanistan and elsewhere is vital and is appreciated by certainly all of us in the US, but I think everyone around the world," he said, adding that his office has been in contact with Doctors Without Borders over this weekend to emphasize that a full and transparent investigation will be conducted.
Carter said he has also issued instruction to ensure that the US makes available, and the coalition in Afghanistan, makes available medical care as possible, and as asked for, for folks in Kunduz.
MSF General Director Christopher Stokes strongly refuted claims from Afghan officials that MSF's hospital in Kunduz was used by the Taliban for military purposes.
"MSF is disgusted by the recent statements coming from some Afghanistan government authorities justifying the attack on its hospital in Kunduz," he said.
"These statements imply that Afghan and US forces working together decided to raze to the ground a fully functioning hospital - with more than 180 staff and patients inside - because they claim that members of the Taliban were present. This amounts to an admission of a war crime," Stokes alleged.
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