By then, Walton said he'd "lost confidence" in the NSA's ability to legally operate the program. He ordered a full review of the surveillance.
In its long report to the surveillance court in August 2009, the Obama administration blamed its mistakes on the complexity of the system and "a lack of shared understanding among the key stakeholders" about the scope of the surveillance.
"The documents released today are a testament to the government's strong commitment to detecting, correcting and reporting mistakes that occur in implementing technologically complex intelligence collection activities, and to continually improving its oversight and compliance processes," Clapper said in a statement Tuesday.
The surveillance court was satisfied by those improvements; it allowed the NSA to continue collecting phone records every day, a practice that continues today.
Now, the Obama administration is fending off lawsuits and a push in Congress to rein in the surveillance.
An unusual coalition of liberal Democrats and Republican civil libertarians has proposed several bills that would either scrap the phone surveillance entirely or require more oversight.
President Barack Obama has said he's open to more oversight but says the surveillance is essential to keep the country safe.
Obama and Clapper have said the changes made in 2009 resulted in tightened controls. American data is still collected but only seldom looked at, officials said. And it is kept on secure computer servers equipped with special software to protect it from analysts looking to illegally snoop.
"There are checks at multiple levels," NSA Deputy Director John Inglis told Congress in July. "There are checks in terms of what an individual might be doing at any moment in time."
The same checks that protect Americans' personal data were also supposed to protect the NSA's information. Yet Snowden, a 29-year-old contractor, managed to walk out with flash drives full of the nation's most highly classified documents.
The NSA is still trying to figure out, in such a complex system, exactly how Snowden defeated those checks.
"I think we can say that they failed," Inglis said. "But we don't yet know where."
Associated Press writers Stephen Braun, Adam Goldman, Kimberly Dozier, Eileen Sullivan, Ted Bridis, Jim Drinkard and Paul Elias in San Francisco contributed to this report.
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