The program traces back to after the Sept. 11 terrorist attacks and came to light in 2013 in leaks by Edward Snowden, the former intelligence contractor.

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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 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 Snowden, the former intelligence contractor.

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.