The humanitarian group Médecins Sans Frontières (MSF) assured the US military its hospital in northern Afghanistan was not under Taliban threat just days before a deadly air strike on the compound last month, the organisation said as it released an internal inquiry into the attack.

The accounts offered by the group seek to bolster its claims that there was no military justification for the air strike on 3 October in Kunduz that killed 30 medical staff members and patients while the city was temporarily in the hands of Taliban fighters. The group has also pushed for an independent investigation into one of the deadliest civilian casualty incidents stemming from a coalition action in the Afghan conflict. The US military and others are conducting parallel reviews into the chain of events leading to the more-than-hour-long attack by an American AC-130 gunship.

“We were running a hospital treating patients, including wounded combatants from both sides,” said the report by the Geneva-based group. “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, asking whether Taliban militiamen were “holed up” in the Kunduz hospital compound or if the staff felt threatened. Mr Stokes said the group replied that there were no armed members of the Taliban on the grounds and the 140-bed hospital was functioning normally. He said there were no follow-up exchanges with the US military, which was aiding Afghan soldiers who were seeking to drive out the Taliban from Kunduz.

The group’s internal report said there were 20 wounded Taliban fighters and five Afghan military forces being treated at the time of the attack. Mr Stokes said there were no weapons inside the compound, dismissing as “ridiculous” claims that the hospital was overrun by Taliban fighters and heavy fighting was under way in the area. The report from MSF said the attack lasted for around an hour, targeting the main hospital building.

It said: “MSF staff recall that the first room to be hit was the ICU [intensive-care unit], where MSF staff were caring for a number of immobile patients, some of whom were on ventilators. Two children were in the ICU. MSF staff were attending to these critical patients in the ICU at the time of the attack and were directly killed in the first air strikes or in the fire that subsequently engulfed the building. Immobile patients in the ICU burnt in their beds.

“Other MSF staff describe seeing people running while on fire and then falling unconscious on the ground. One MSF staff was decapitated by shrapnel in the air strikes.”

Three US strikes – on a warehouse, a mansion and the hospital – 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.