Six US troops were killed when the Blackhawk chopper went down in Zabul province on December 17, but the precise circumstances around the crash have been the subject of confusion.
"The families of the soldiers killed in the December 17 helicopter crash have been notified that enemy action caused the crash and loss of life," the NATO-led International Security Assistance Forces said in an email to AFP.
"The investigation is ongoing, and more details will be provided when the investigation is complete," ISAF said.
CNN first reported the military's new version of events.
In the hours after the crash, US officers suggested the helicopter went down due to a mechanical failure but that the crew may have come under fire once the chopper crashed. But officials later backed away from that account, ruling out any enemy fire.