At least 30 people were killed when the hospital in Kunduz was hit by the strike on Oct. 3 while Afghan government forces were battling to regain control of the northern city from Taliban forces who had seized it days earlier.
The United States has said the hospital was hit by accident and two separate investigations by the U.S. and NATO are underway but the circumstances of the incident, one of the worst of its kind during the 14-year conflict, are still unclear.
MSF General Director Christopher Stokes told reporters the organization was still awaiting an explanation from the U.S. military.
"All the information that we've provided so far shows that a mistake is quite hard to understand and believe at this stage," he said while presenting an MSF internal report on the incident.
The report said many staff described "seeing people being shot, most likely from the plane" as they tried to flee the main hospital building.
"From what we are seeing now, this action is illegal in the laws of war," Stokes said. "There are still many unanswered questions, including who took the final decision, who gave the targeting instructions for the hospital."
Several Afghan officials have suggested Taliban fighters were using the hospital as a base, a claim that MSF firmly rejects. It says the facility was under its control at all times and there were no armed fighters present either before or during the attack.
The hospital was treating wounded combatants from both sides as well as civilians, but the group says it always maintained a strict policy of neutrality between the two sides.
"Treating wounded combatants is not a crime," Stokes said.
MSF says the site's location had been clearly communicated to both Afghan forces and the Taliban and it was clearly identifiable as a hospital.
"That night, it was one of the few buildings with electrical power, it was fully lit up," Stokes said.
He also said that inspections of the area around the hospital since the Taliban withdrew from Kunduz last month did not reveal signs of heavy fighting.
MSF, called Doctors Without Borders in English, has revised the original casualty figure upwards and now says 30 people, including 13 staff members and three children were killed during repeated attacks by a powerful U.S. gunship.
The U.S. investigation is headed by a U.S. general and two brigadier generals.
A separate NATO casualty report into the incident, originally expected in October, has been delayed while the investigation continues, U.S. Defense Secretary Ash Carter announced last month.