"It was a virus that we believe at this point entered from the wild, if you will, not specifically targeted at the RPA (remotely piloted aircraft) activities but entered through some other process," General Robert Kehler
"We're not quite sure how that happened yet," he said.
Discovered in mid-September at Creech Air Force base in
Nevada, the virus infected computers in the ground control system for the drones, which is separate from the drones' flight control system.
Drone flights in Afghanistan and other war zones directed from the Creech base were not affected by the virus, according the US Air Force.
One possible route for the virus could have come through hard drives in the ground control system, as the removable drives are used to transfer data and moved from "machine to machine," Kehler said.
"So that opens the possibility to get something introduced in the system," he said.
Wired magazine, which first reported the problem, had said the virus spread through removable hard drives used to load map updates and transfer mission videos from one computer to another.
In this case, Kehler said cyber security safeguards had performed successfully.
"All the information that I have would suggest that the systems that we have put in place to detect such viruses worked," he said.
"We were able to quarantine the virus fairly quickly, we are still doing cleaning activities in some isolated machinery."
The general added that US military networks are constantly being probed by outsiders.
"We see multiple deliberate attempts to try to get into our networks, almost daily."
The US military's newly created cyber command falls within Kehler's Strategic Command, which also oversees the country's nuclear arsenal.