Washington (CNN) -- The systems that control U.S. military drones have been infected with a computer virus, a U.S. defense official confirmed to CNN on Monday.
Despite the infection of the classified program, the virus has not "stopped flights worldwide," the official said.
The official declined to comment on how the systems were infected nor whether the virus has resisted attempts to remove it.
The infection was first reported by Noah Shachtman for Wired magazine last week.
"Military officials are more concerned than panicked by this virus. They're just really not sure what's going on. They're not sure if it's a deliberate attack. They're not sure if it's something accidental," he said.
While drones are flown on missions in war zones such as Iraq and Afghanistan, the actual "cockpit" of the unmanned aircraft is on U.S. soil -- the operators work at Nevada's Creech Air Force Base.
According to Wired, the virus, which records pilot key strokes, was first detected about two weeks ago. Tech specialists are unsure whether it was installed intentionally, Wired reported.
Shachtman said the military has had a hard time wiping out the virus.
"They're tried over and over again to get rid of this thing using some fairly conventional methods, and they haven't worked. And so it seems the only thing to get rid of this virus is to basically wipe the hard drives of these computers entirely and sort of rebuild the computers from scratch," he said.
But that can be an exhausting process.
In 2008, removable hard drives introduced a virus into thousands of Defense Department computers, and to this day the Pentagon is still purging some machines.
In the case of the computers that help coordinate the drones, care also has to be taken to back up all the information so it isn't lost during rebuilding.
U.S. drone strikes have been responsible for the deaths of dozens of suspected militants. In recent years, the United States has sharply increased its used of unmanned planes to target insurgents in Pakistan's tribal region, a volatile area bordering war-torn Afghanistan. The covert CIA drone program has been deeply unpopular with many Pakistanis, who say the attacks kill civilians and violate their country's sovereignty.
In August, a drone attack killed al Qaeda No. 2 Atiya Abdul Rahman in Pakistan. The most recent high-profile drone strike resulted in the death of U.S.-born militant cleric Anwar al-Awlaki in Yemen last month.
Unmanned aerial vehicles have become indispensable for military planners who depend on constant combat air patrols. But current and former Pentagon officials admit the technology cuts both ways.
At the confirmation hearing for Defense Secretary Leon Panetta, former Deputy Defense Secretary William Lynn said bluntly, "In the 21st century, bits and bytes can be as threatening as bullets and bombs."
He said even the National Defense University has been breached, and in a single intrusion this year 24,000 files were taken from a defense company.
"Some of the stolen data is mundane, like the specifications for small parts of tanks, airplanes and submarines. But a great deal of it concerns our most sensitive systems, including avionics, surveillance technologies, satellite communications systems and network security protocols," he said.
Perhaps most alarming, Lynn admitted that up till now, the U.S. military had been unable to secure its systems.
"Current countermeasures have not stopped this outflow of sensitive information," Lynn said. "We need to do more to guard our digital storehouses of design innovation."
Officials have not yet determined whether the virus introduced into the drone program is benign, or doing actual harm. An investigation is ongoing.
Despite the fact the controls are not linked into any outside network, and therefore seemingly impervious to intrusion, the drone systems do have security issues. Shachtman said they still use external hard drives, and when they're attached to top-secret computers they can open them up to infection.
He said the true danger of the virus comes not from an ability to "bring down a drone," which is unlikely, but from an erosion of trust.
If officials come to think that the information they're receiving from the unmanned vehicles has been compromised, they're much less likely to view it as safe and valuable, he surmised.