Christopher Stokes, general director of Doctors Without Borders, at a news conference Thursday in Kabul. (Aref Karimi/AFP/Getty Images)

After nearly an hour of bombing on its hospital in the Afghan city of Kunduz, a Doctors Without Borders representative in Kabul received a text message from a U.S. military official in response to the group’s pleas to stop the attack: “I’ll do my best,” said the message from the American, who was also in Kabul. “Praying for you all.”

The 2:59 a.m. message is included in a log released Thursday by Doctors Without Borders in a report on the Oct. 3 bombing of its Kunduz medical facility by the U.S. military. The first bombs from an AC-130 gunship fell between 2 a.m. and 2:08 a.m., prompting a flurry of calls from the medical organization, also known as Médecins Sans Frontières Global (MSF), for the airstrikes to stop.

The report was released by MSF to be transparent and to counter speculation that the hospital was being used as a Taliban military base, the medical organization said. The hospital was treating Afghan soldiers, Taliban fighters and civilians the night of the airstrikes, it said.

The bombing came as the U.S. and Afghan militaries fought to take back Kunduz, which had fallen to the Taliban a few days before. Some 30 medical staff members and patients were killed, with some burned beyond recognition.

Just days before the airstrike, the humanitarian group assured the U.S. military that the hospital in northern Afghanistan was not under Taliban threat, MSF said as it released the internal probe into the attack.

The Geneva-based group also has pushed for an independent investigation into one of the deadliest civilian casualty incidents stemming from a coalition action in the Afghan conflict. The U.S. military and others are conducting parallel reviews into the chain of events leading to the more than hour-long attack by the American gunship.

“What we know is that we were running a hospital treating patients, including wounded combatants from both sides,” MSF’s report said. “This was not a ‘Taliban base.’ ”

In Kabul, the group’s general director, Christopher Stokes, told reporters that the Pentagon had been in direct contact just days before the attack to ask whether Taliban militiamen were “holed up” in the Kunduz hospital compound and whether the staff felt threatened.

Stokes said MSF replied that there were no armed Taliban on the grounds and the 140-bed hospital was functioning normally.

“There was no following” dialogue from the U.S. military “saying, ‘We have different information. We are going to bomb you,’ ’’ Stokes said.

MSF’s report said there were 20 wounded Taliban fighters and five Afghan military personnel being treated in the hospital at the time of the attack. Stokes said there were no weapons inside the compound and dismissed as “ridiculous” claims that the hospital was overrun by Taliban fighters and heavy fighting was underway in the area.

“They were patients and they were in their beds,” Stokes said of the Taliban patients.

Three U.S. strikes — on the hospital and on a warehouse and a mansion in densely populated residential areas — were requested by Afghan commanders, who say they asked for help because their forces were under attack by Taliban fighters. But residents interviewed by The Washington Post said there were no militants at any of the locations at the time of the attacks.

“The question remains as to whether our hospital lost its protected status in the eyes of the military forces engaged in this attack — and, if so, why,” the report said. “The answer does not lie within the MSF hospital. Those responsible for requesting, ordering and approving the airstrikes hold these answers.”

Murphy and Lamothe reported from Washington.

Read more:

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The Pentagon’s evolving response to the Afghan hospital attack

Top U.S. general in Afghanistan: Hospital ‘mistakenly struck’