US intelligence officials have released secret documents showing that a judge reprimanded the National Security Agency in 2009 for violating its own procedures and misleading the nation's intelligence court about how it used the telephone call logs that it gathers.
It was the second severe scolding of the spy agency by the Foreign Intelligence Surveillance Court (FISC) to come to light since the disclosure of thousands of NSA documents by Edward Snowden, a former NSA contractor, began this summer.
The newly disclosed violations involved the NSA programme that has drawn perhaps the sharpest criticism from members of Congress and civil libertarians - the collection and storage for five years of information on virtually every phone call in the United States.
The agency uses orders from the intelligence court to compel phone companies to turn over records of numbers called and the time and duration of each call - the "metadata", but not the actual content of the calls.
Since Snowden disclosed the programme, the agency has said that while it gathers data on billions of calls, it makes only a few hundred queries in the database each year, when it has "reasonable, articulable suspicion" that a telephone number is connected to "terrorism".
But the new documents, released on Tuesday, show the agency also compares each day's phone call data as it arrives with an "alert list" of thousands of domestic and foreign phone numbers it has identified as possibly linked to "terrorism".
Declarations by the agency to the court that all the numbers on the alert list had met the legal standard of suspicion were false, officials said. In fact, only about 10 per cent of 17,800 phone numbers on the alert list in 2009 had met the test, they said.
In a sharply worded ruling in March 2009, judge Reggie Walton criticised the NSA's failure to comply with rules set by the intelligence court to set limits on how it could use the data it had gathered, and accused the agency of repeatedly misinforming judges.
"The government has compounded its non-compliance with the court's orders by repeatedly submitting inaccurate descriptions of the alert list process" to the court, Walton wrote. "It has finally come to light that the FISC's authorisations of this vast collection programme have been premised on a flawed depiction of how the NSA uses" the phone call data. A senior US intelligence official, briefing reporters before the documents' release, admitted the sting of the court's reprimand, but said the problems came in a complex, highly technical programme and were unintentional. "There was nobody at NSA who really had a full understanding of how the programme was operating at the time," said the official. The official noted that the agency itself discovered the problem, reported it to the court and to Congress and worked out new procedures that the court approved.
In making public 14 documents on the website of the director of national intelligence, James Clapper, the intelligence officials were acting in response to Freedom of Information Act lawsuits and a call from President Barack Obama for greater transparency about intelligence programmes.
The lawsuits were filed by two advocacy groups, the Electronic Frontier Foundation and the American Civil Liberties Union.
"The documents only begin to uncover the abuses of the huge databases of information the NSA has of innocent Americans' calling records," said Mark Jaycox, a policy analyst at the Electronic Frontier Foundation.
He said the agency's explanation - that none of its workers fully understood the phone metadata programme - showed "how much of a rogue agency the NSA has become".
Walton's ruling, originally classified as top secret, did not go that far. But he wrote that the privacy safeguards approved by the court "have been so frequently and systematically violated" that they "never functioned effectively".
Senator Patrick Leahy, chairman of the Senate Judiciary Committee, said the documents showed "systemic problems" and that the bulk collection of phone records should stop.