Masoom Stanekzai told The Associated Press in an interview that Taliban insurgents and possibly Pakistani operatives of the government's secret service were using the facility in Kunduz city as a "safe place."
The hospital was bombed by a US AC-130 gunship in the early hours of October 3, killing at least 22 people and injuring many more. The main building was destroyed and the hospital is no longer operating.
Kate Stegeman, MSF's communications director in Afghanistan said today: "We reiterate that every staff member in Kunduz working for MSF has repeatedly reported to us that there were no armed people in the hospital at the time of the bombing."
Stanekzai said a Taliban flag had been hoisted on the walls around the hospital compound.
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"That was a place they wanted to use as a safe place because everybody knows that our security forces and international security forces were very careful not to do anything with a hospital," Stanekzai said. "But when there was on one of the walls of the hospital, there was a Taliban flag what can you think?"
Taliban fighters took control of Kunduz on September 28 in a multi-pronged surprise attack. What followed was a three-day looting and killing spree that ended when government forces launched a counter offensive on October 1.
The hospital was bombed repeatedly just after 2 am on October 3. President Barack Obama apologized for the bombing and the commander of US and NATO forces in Afghanistan, Gen. John F Campbell said it was a mistake. He said airstrike had been called in by Afghan forces.