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KABUL, Afghanistan (AP) — Afghanistan’s acting defense minister said Monday that the Doctors Without Borders hospital bombed by U.S. forces in the northern city of Kunduz was being used by insurgents as a “safe place.”

The hospital was bombed by a U.S. AC-130 gunship in the early hours of Oct. 3, killing at least 22 people and wounding many more. The main building was destroyed and the hospital has been shut down.

“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,” Defense Minister Masoom Stanekzai told The Associated Press, adding that a Taliban flag had been mounted on one of the hospital’s walls.

Doctors Without Borders, also known by its French acronym MSF, has repeatedly denied that Taliban fighters were present in the hospital compound at the time of the attack.

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“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,” Kate Stegeman, MSF’s communications director in Afghanistan, said Monday: The group said no staff had reported a Taliban flag on any wall of the compound.

MSF has acknowledged that it treated wounded Taliban fighters at the Kunduz hospital, but it insists no weapons were allowed in. Afghans who worked there have told the AP that no one was firing from within.

But Stanekzai insisted that “the compound was being used by people who were fighting there, whether it was Taliban or ISI or whoever they were,” referring to Pakistan’s powerful Inter-Services Intelligence agency, long accused by Kabul of supporting the Taliban. “If the fighting was not coming from there, that kind of a mistake will never happen.”

Taliban fighters seized Kunduz on Sept. 28 in a multi-pronged surprise attack. Government forces launched a counteroffensive three days later and were eventually able to drive the insurgents out.

The hospital was bombed repeatedly just after 2 a.m. on Oct. 3. President Barack Obama apologized for the bombing and the commander of U.S. and NATO forces in Afghanistan, Gen. John F. Campbell, said it was a mistake. He said the airstrike had been called in by Afghan forces.

The incident is being investigated by the U.S. military, NATO and by the Afghan government as part of its probe into how the Taliban were able to take over the provincial capital, the first major urban center they’ve taken since a U.S. invasion toppled their regime in 2001. Preliminary details of the NATO investigation are expected in the coming days.

American special operations analysts were scrutinizing the MSF hospital days before it was destroyed because they believed it was being used by a Pakistani operative to coordinate Taliban activity, officials have told the AP. The analysts knew it was a medical facility, according to a former intelligence official who is familiar with some of the documents describing the site.

It’s unclear whether that information ever got to commanders who ordered the deadly airstrike.

The analysts had assembled a dossier that included maps with the hospital circled, along with indications that intelligence agencies were tracking the location of a Pakistani operative and activity reports based on overhead surveillance, according to the former intelligence official. The intelligence suggested the hospital was being used as a Taliban command and control center and may have housed heavy weapons.

After the attack, some U.S. analysts assessed that the strike had been justified and concluded the Pakistani, believed to have been with the ISI, had been killed.

No evidence has surfaced publicly suggesting a Pakistani died in the attack, and MSF says none its staff was Pakistani. The former intelligence official was not authorized to comment publicly and spoke on condition of anonymity.

The new details about the military’s suspicions complicate an already murky picture of one of the worst civilian casualty incidents of the Afghan war. They also raise the possibility of a breakdown in intelligence sharing and communication across the military chain of command.

MSF, a Nobel Peace Prize-winning organization that provides medical aid in conflict zones, has called for an investigation by the International Humanitarian Fact-Finding Commission, based in the Swiss capital, Bern. An IHFFC investigation needs the cooperation of both Afghanistan and the U.S. before it can proceed, which neither government is expected to give.

Stanekzai said Afghanistan will not support the sort of investigation that MSF has demanded. “If you increase the number of commissions and investigating teams, that will make it more complicated instead of getting into the facts. Already there are three investigations; how many more do you need?” he said.

Stanekzai said his government had evidence the insurgents in Kunduz were communicating with command and control centers in Pakistan. “We have traced very clearly the communications they were receiving from Quetta, Peshawar and Karachi,” he said, naming three Pakistani cities where the Afghan Taliban presence is widely known.

“How can any country allow the nationals of other countries to have such large-scale operations from their soil and just sit and watch them,” Stanekzai said.

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Associated Press intelligence writer Ken Dilanian in Washington contributed to this report.