WASHINGTON >> A federal judge on Monday partly blocked the National Security Agency’s program that systematically collects Americans’ domestic phone records in bulk just weeks before the agency was scheduled to shut it down and replace it. The judge said the program was most likely unconstitutional.

In a separate case challenging the program, a federal appeals court in New York on Oct. 30 had declined to weigh in on the constitutional issues, saying it would be imprudent to interfere with an orderly transition to a replacement system after Nov. 29.

But on Monday, in a 43-page ruling, Judge Richard J. Leon of U.S. District Court for the District of Columbia wrote that the constitutional issues were too important to leave unanswered in the history of the program, which traces back to after the Sept. 11 terrorist attacks and came to light in 2013 in leaks by Edward J. Snowden, the former intelligence contractor.

"With the government’s authority to operate the bulk telephony metadata program quickly coming to an end, this case is perhaps the last chapter in the judiciary’s evaluation of this particular program’s compatibility with the Constitution," he wrote. "It will not, however, be the last chapter in the ongoing struggle to balance privacy rights and national security interests under our Constitution in an age of evolving technological wizardry."

Under the program, the NSA has been collecting Americans’ phone records in bulk from telephone companies. It uses the data to analyze social links between people to hunt for hidden associates of terrorism suspects.

Leon specifically ordered the NSA to stop collecting phone records for one customer of Verizon: a lawyer in California and his law firm. But he did so, he wrote, knowing that the Justice Department had said that blocking the collection of just one person’s records might require shutting down the entire program because it would be technically difficult to screen him out.

The Justice Department said it was reviewing the decision but had no comment about whether it would appeal the injunction. Reuters reported on Monday that the NSA had sent a memo to Congress saying that testing of the replacement system had begun.

The program began based on a unilateral claim of executive power by President George W. Bush. In 2006, the Justice Department persuaded the Foreign Intelligence Surveillance Court to begin issuing orders for the program under an interpretation of a provision of the USA Patriot Act that permits collection of business records relevant to a national-security investigation.

In June 2013, Snowden leaked one such order to a subsidiary of Verizon. After substantial debate, Congress in June enacted the USA Freedom Act, which banned bulk collection under the Patriot Act after Nov. 29, and established a system under which the bulk data will stay with the phone companies but the NSA can swiftly access it.

Revelations of the program set off lawsuits challenging it as illegal on statutory and constitutional grounds. In December 2013, Leon ruled that it was most likely unconstitutional but issued no order, permitting the Court of Appeals for the District of Columbia to review his ruling.

But a week later in a different case, a federal judge in New York ruled that the program was legal. The federal appeals court in New York eventually ruled that the program was not based on a legitimate interpretation of the Patriot Act, but sidestepped the constitutional question.

Leon’s ruling that the bulk collection of calling records most likely violated the Constitution was novel because in 1979, the Supreme Court held that call logs or metadata — records showing who called whom and when, but not the content of what they said — was not protected by the Fourth Amendment.

Its ruling turned on the notion that people have no reasonable expectation of privacy for information they reveal to a third party, and they expose whom they are calling to phone companies. That case, however, involved one criminal suspect’s calls over several days, not call records of everyone in the country and the storage of them for five years.

Leon argued that changing technological capabilities had brought call records into the ambit of Fourth Amendment protections. But last summer, an appeals court overturned his ruling on a technicality: There was not enough evidence that the plaintiffs in the case — including Larry Klayman, the conservative legal activist — had their calls collected by the program. Klayman was a not a customer of the Verizon subsidiary in the order Snowden leaked.

The appeals court sent the case back to Leon, who suggested to Klayman that he add a plaintiff who was a customer of the Verizon subsidiary. He did so: J.J. Little, a trial lawyer in California, and his law firm.

Leon issued the injunction on Monday for Little’s records, not Klayman’s.

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