“There was nobody at N.S.A. who really had a full understanding of how the program was operating at the time,” said the official, who spoke on the condition of anonymity. 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 Web site of the director of national intelligence, James R. Clapper Jr., the intelligence officials were acting in response to Freedom of Information Act lawsuits and a call from President Obama for greater transparency about intelligence programs. 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 N.S.A. has of innocent Americans’ calling records,” said Mark M. 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 program — showed “how much of a rogue agency the N.S.A. has become.”

Judge 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 J. Leahy of Vermont, the chairman of the Senate Judiciary Committee, welcomed the release of the documents, but said that they showed “systemic problems” and that the bulk collection of Americans’ phone records should be stopped.

Intelligence officials have expressed some willingness to adjust the program in response to complaints from Congress and the public, possibly by requiring the phone companies, rather than the N.S.A., to stockpile the call data. But they say that the program remains crucial in detecting terrorist plots and is now being run in line with the court’s rules.

A different intelligence court judge, John D. Bates, rebuked the N.S.A. in 2011 for violations in another program and also complained of a pattern of misrepresentation. The 2011 opinion, which made a reference to the 2009 reprimand, was released by intelligence officials last month.