"All the information that we've provided so far shows that a mistake is quite hard to understand and believe at this stage," MSF General Director Christopher Stokes told reporters while presenting the group's internal report on the incident, Reuters reported on Thursday.
The report said many staff described "seeing people being shot, most likely from the plane" as they tried to flee the main hospital building, which was under attack by US military aircraft.
At least 30 people were killed when the hospital in Kunduz was hit by a powerful US attack aircraft on October 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 US 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.