“You could theoretically ground everybody,” Haines said.
Haines and a fellow hacker put data that would be used in the FAA system, known as NextGen, into a flight simulator to show what could happen if the system is hacked.
“We were able to create a flight…we were able to take off from SFO [San Francisco] circle back over the bay, come back and buzz the tower,” Haines explained.
“If I suddenly injected 50 extra flights onto their radar screen that they hadn’t expected, they’re going to be panicking trying to figure out what’s going on,” he said.
University of Texas professor Todd Humphreys is an expert on navigation systems, and thinks Haines is onto something.
“It ought to be obvious to the FAA. This is an obvious problem. This is something that’s using antiquated technology from the 1980s,” said Humphreys.
Haines said he brought his evidence to the FAA, but claimed they ignored him.
CNBC reached out to the FAA about his claims, and a spokesman said the agency has a thorough process in place to identify and mitigate risks in the system…the process is ongoing…and there are backups to ensure safe operations.
In the statement, the FAA declined to say what risks it has identified, saying that information is “security sensitive.”
By CNBC’s Scott Cohn; Follow him on Twitter @ScottCohnCNBC