The NSA sought to explain away the "compliance incident" before the Foreign Intelligence Surveillance Court ruling, saying no one at the agency fully understood how its own program worked.
Judge Reggie Walton said in a scathing rebuke the NSA's explanation of the violations "strains credulity."
The improper activity went on from May 2006 until January 2009, when Walton, the secret court's presiding judge, put a stop to it and ordered the program's overhaul in the final days of the George W. Bush administration.
The court, which issues warrants and sets rules for collecting foreign intelligence inside the United States, ruled in 2006 the NSA must have a "reasonable articulable suspicion" each phone number being targeted is associated with a terrorist organization.
But over the three years, only 1,935 of the 17,835 phone numbers checked against phone records were based on that reasonable-suspicion standard, intelligence officials cited by The Wall Street Journal said.
Walton -- whose court is known as the FISA Court, after the Foreign Intelligence Surveillance Act that established it -- said in a March 2009 ruling the NSA had so "frequently and systematically violated" the practices and procedures it said it was following that a vital part of the program "never functioned effectively."
The judge in his opinion released Tuesday criticized "repeated inaccurate statements made in the government's submissions."
Officials had told the court the violations were unintentional, explaining NSA officials didn't understand their own records-collection program.
"From a technical standpoint, there was no single person who had a complete technical understanding of the [record] system architecture," NSA Director Keith Alexander said in a Feb. 13, 2009, declaration to the judge.
Alexander and other intelligence officials have sought to reassure lawmakers and the public the phone-records program, as sweeping as it sounds, is vigilantly executed under the court's strict oversight.
"This is not a program where we are out freewheeling it," Alexander told the House Intelligence Committee June 13. "It is a well-overseen and a very focused program."
His testimony came a week after the first disclosure by former NSA contractor Edward Snowden of the massive phone records collection.
Key lawmakers on Capitol Hill renewed their calls Tuesday to shut down the NSA's phone-data program.
"We have said before that we have seen no evidence that the bulk collection of Americans' phone records has provided any intelligence that couldn't be gathered through less intrusive means and that bulk collection should be ended," Sens. Ron Wyden, D-Ore., and Mark Udall, D-Colo., said in a statement.
"These documents provide further evidence that bulk collection is not only a significant threat to the constitutional liberties of Americans, but that it is a needless one," they said.
Significant additional violations, "particularly about violations pertaining to the bulk email records collection program," remain classified, the senators said.
The violations outlined the declassified documents were uncovered by the Justice Department after a Jan. 9, 2009, NSA meeting, the documents indicate. The government told the FISA Court about them Jan. 15.
National Intelligence Director James Clapper said the discovery and reporting of the privacy violations proved NSA oversight worked.
The released documents "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 wrote in a cover note accompanying the released documents.
Officials made the violations public in compliance with a court order stemming from lawsuits against the Justice Department by civil liberties groups and at President Obama's direction following Snowden's leaks.
The court ruling was one of more than a dozen documents declassified and released. The release included roughly 1,800 pages.
The redacted documents can be viewed at tinyurl.com/UPI-Declassified-Documents.