U.S. intelligence agencies conducted illegal surveillance on American citizens over a five-year period, a practice that earned them a sharp rebuke from a secret court that called the matter a “very serious” constitutional issue.

The criticism is in a lengthy secret ruling that lays bare some of the frictions between the Foreign Intelligence Surveillance Court and U.S. intelligence agencies obligated to obtain the court’s approval for surveillance activities.

The ruling, dated April 26 and bearing the label “top secret,” was obtained and published Thursday by the news site Circa.

It is rare that such rulings see the light of day, and the lengthy unraveling of issues in the 99-page document opens a window on how the secret federal court oversees surveillance activities and seeks to curtail those that it deems overstep legal authority.

The document, signed by Judge Rosemary M. Collyer, said the court had learned in a notice filed Oct. 26, 2016, that National Security Agency analysts had been conducting prohibited queries of databases “with much greater frequency than had previously been disclosed to the court.”

It said a judge chastised the NSA’s inspector general and Office of Compliance for Operations for an “institutional ‘lack of candor’ ” for failing to inform the court. It described the matter as “a very serious Fourth Amendment issue.”

The Fourth Amendment protects people from unreasonable searches and seizures by the government, and is a constitutional bedrock protection against intrusion.

Parts of the ruling were redacted, including sections that give an indication of the extent of the illegal surveillance, which the NSA told the court in a Jan. 3 notice was partly the fault of “human error” and “system design issues” rather than intentional illegal searches.

The NSA inspector general’s office tallied up the number of prohibited searches conducted in a three-month period in 2015, but the number of analysts who made the searches and the number of queries were blacked out in the ruling.

The NSA gathers communications in ways known as “upstream” and “downstream” collection. Upstream collection occurs when data are captured as they move through massive data highways – the internet backbone – within the United States. Downstream collection occurs as data move outside the country along fiber optic cables and satellite links.

Data captured from both upstream and downstream sources are stored in massive databases, available to be searched when analysts need to, often months or as much as two years after the captures took place.

The prohibited searches the court mentioned involved NSA queries into the upstream databanks, which constitute a fraction of all the data NSA captures around the globe but are more likely to contain the emails and phone calls of people in the United States.

Federal law empowers the NSA and CIA to battle foreign terrorist actions against the United States by collecting the electronic communications of targets believed to be outside the country. While communications of U.S. citizens or residents may get hoovered up in such sweeps, they are considered “incidental” and must be “minimized” – removing the identities of Americans – before broader distribution.

The court filing noted an NSA decision March 30 to narrow collection of “upstream” data within the United States. Under that decision, the NSA acknowledged that it had erred in sweeping up the communications of U.S. citizens or residents but said those errors “were not willful.” Even so, the NSA said it would no longer collect certain kinds of data known as “about” communications, in which a U.S. citizen was merely mentioned.

The NSA announced that change publicly on April 28, two days after the court ruling, saying the agency would limit its sweeps to communications either directly to or from a foreign intelligence target. That change would reduce “the likelihood that NSA will acquire communications of U.S. persons or others who are not in direct contact with one of the agency’s foreign intelligence targets.”

The court document also criticized the FBI’s distribution of intelligence data, saying it had disclosed raw surveillance data to sectors of its bureaucracy “largely staffed by private contractors.”

The “contractors had access to raw FISA information that went well beyond what was necessary to respond to the FBI’s requests,” it said, adding that the bureau discontinued the practice on April 18, 2016.

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