The US forces had the exact coordinates of the clinic before launching an aerial assault on October 3 that killed 30 people, including 13 staff members, 10 patients and 7 unidentified bodies, the report by the international medical charity, known by its French acronym MSF, said.
The Pentagon said it is studying the report by the MSF.
"Since this tragic incident, we have worked closely with MSF to determine the facts surrounding it. Just yesterday, Resolute Support commander Gen John Campbell met personally with MSF representatives," Pentagon spokesman Capt Jeff Davis told reporters.
The US is also committed to working with MSF to determine the full extent of the damage to the hospital, so that it can be repaired in full, Davis said.
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In its report, the MSF reiterated its call for an international investigation.
The chronological review of the events leading up to, during, and immediately following the airstrikes show no reason why the hospital should have come under attack, it said.
"The view from inside the hospital is that this attack was conducted with a purpose to kill and destroy," said Christopher Stokes, MSF General Director.
"But we don't know why. We neither have the view from the cockpit, nor the knowledge of what happened within the US and Afghan military chains of command," the report said.
Among the 105 patients at the time of the airstrikes, MSF was treating wounded combatants from both sides of the conflict in Kunduz, as well as women and children, it said.
"Wounded combatants are patients under international law, and must be free from attack and treated without discrimination. Medical staff should never be punished or attacked for providing treatment to wounded combatants," he argued.
The MSF internal review describes patients burning in their beds, medical staff that were decapitated and had lost limbs, and others who were shot from the air while they fled the burning building.