The National Security Agency (NSA) during the last years of the George W. Bush administration committed “flagrant” violations of Americans’ privacy rights by conducting illegal searches of phone records, according to newly disclosed government documents.

Officials in the Obama administration released 14 documents that showed a judge serving on the Foreign Intelligence Surveillance Court (FISC) reprimanded the NSA four years ago for going through the phone records of Americans from 2006 to 2009 without proper authorization.

Judge Reggie Walton criticized the government for not following its own procedures and for “what appears to be a flagrant violation” of a court order that allowed for the sifting of phone records belonging to individuals suspected of terrorist ties. The NSA reportedly went beyond this threshold on a “daily basis” by going through the records of Americans not linked to terrorism for the three years in question.

Privacy safeguards put in place by the court “have been…frequently and systematically violated” by the NSA, wrote the judge. He demanded that someone with the “authority to speak on behalf of the Executive Branch” explain why the violations occurred and over what period of time.

Walton’s scolding represented the second time recently that the spy agency had come under fire by a FISC judge since whistleblower Edward Snowden disclosed thousands of NSA documents about its domestic surveillance programs. A different intelligence court judge, John D. Bates, reprimanded the NSA in 2011 for violations it committed in another program, and said he found a pattern of misrepresentation by the agency.

NSA officials have argued that they make only a few hundred queries annually into a database containing billions of calls, and that those queries are based on “reasonable, articulable suspicion” that a telephone number is connected to terrorism.

The documents released this week by the Office of the Director of National Intelligence show that the NSA also compared the daily collection of phone calls with an “alert list” containing thousands of domestic and foreign phone numbers possibly linked to terrorism.

The New York Times reported that the NSA “told the court that all the numbers on the alert list had met the legal standard of suspicion, but that was false.” In reality, only about 10% of 17,800 phone numbers on the list in 2009 had met that test, a senior intelligence official told the newspaper on the condition of anonymity.

In an effort to defend the agency, the same official said: “There was nobody at NSA who really had a full understanding of how the program was operating at the time.”

The official also said the NSA discovered the problem on its own, reported it to the FISC and to Congress, and created new procedures approved by the court.

The latest revelation demonstrated “how much of a rogue agency the NSA has become,” Mark M. Jaycox, a policy analyst at the Electronic Frontier Foundation (EFF), told the Times. “The documents only begin to uncover the abuses of the huge databases of information the NSA has of innocent Americans’ calling records.”

The previously classified documents were released in response to Freedom of Information Act lawsuits filed by the EFF and the American Civil Liberties Union.

EFF had attempted to have these documents released two years ago, but “at that time, the government withheld every word, claiming that grave harm to national security would result if the court’s opinions were released,” EFF senior counsel David Sobel told The Washington Post. “Now that the agency has been forced to release them, we can see that the real reason for secrecy was to conceal the fact that surveillance under the Patriot Act (pdf) was far broader, and less focused, than the public and Congress had been led to believe.”

Now, NSA has made a “breathtaking admission,” said EFF in a prepared statement, “that the NSA's surveillance apparatus, for years, was so complex and compartmentalized that no single person could comprehend it."

-Noel Brinkerhoff, Danny Biederman

To Learn More:

Court Upbraided N.S.A. on Its Use of Call-Log Data (by Scott Shane, New York Times)

Declassified Court Documents Highlight NSA Violations in Data Collection for Surveillance (by Ellen Nakashima, Julie Tate and Carol Leonnig, Washington Post)

NSA Blasted for 'Flagrant Violation' of Privacy (by Adam Klasfeld, Courthouse News Service)

DNI Clapper Declassifies Intelligence Community Documents Regarding Collection Under Section 501 of the Foreign Intelligence Surveillance Act (FISA) (Office of the Director of National Intelligence)

Foreign Intelligence Surveillance Court Document (pdf)

Obama Assurance of Surveillance Oversight is undercut by FISA Court’s Chief Judge (by Noel Brinkerhoff, AllGov)          

Judicial Oversight of U.S. Spying Rests with One Man…John Roberts (by Noel Brinkerhoff, AllGov)