"In an effort for those in the intelligence community to be able to share with each other, there was an enormous amount of information concentrated in once place. That's a mistake," he told attendees at the Aspen Security Forum in Colorado. "The loading of everything onto a server creates a risk."
NSA chief, Gen. Keith Alexander, has explained that Snowden accessed much of the information on a single internal site designed to share information.
Carter said they are working to limit that access, as well as implementing a "two-man rule" everywhere systems administrators have "elevated" clearance access to sensitive information.
He said they are also looking at how to better monitor individuals with access to that kind of information and suggested the Pentagon might monitor intelligence workers just as it monitors staff at nuclear installations.
"When it comes to nuclear weapons, you watch people's behavior in a special way. We don't let people all by themselves do anything," he said. "There is always some aberrant individual and you've got to recognize that."
Meanwhile, Carter said the Pentagon is also close to launching a 4,000-person cybersquad of both offensive and defensive teams. He said the teams will both protect Defense Department systems and launch cyberattacks against enemy networks.