A federal judge has outlawed the FBI’s practice of forcing recipients of national security-related subpoenas to keep the requests secret.

A court decision yesterday by Judge Victor Marrero of U.S. District Court in Manhattan calls into question the future of the FBI’s increasing reliance on an investigative tool known as a “national security letter.”

The FBI has had this subpoena power since 1986, although the USA Patriot Act legislation of 2001 greatly expanded the bureau’s authority to send such letters, which, unlike warrants and grand jury subpoenas, are issued without court oversight.

The letters, which are used exclusively to assist in terrorism or spy investigations, often seek telephone and Internet records. An internal Justice Department report concluded this year that some letters were being issued without proper authorization by senior FBI officials. But Judge Marrero’s concerns relate exclusively to the law permitting such letters to carry a gag order, preventing recipients from disclosing that they ever received a letter. In an earlier decision in 2004, Judge Marrero ruled that the gag order — which was construed to prohibit even discussions about the subpoena with a lawyer — violated the First and Fourth Amendments to the Constitution.

The decision yesterday ruled that Congress has further exacerbated the issue, from a constitutional perspective, with the 2006 Patriot Reauthorization Act. Now, the FBI makes a case-by-case decision as to whether to prohibit disclosure of a national security letter.

Under the new law, recipients can go to court to challenge the gag order. But in deciding whether to lift the gag order, judges are required by the amended Patriot Act to accept, without challenge, a statement from the FBI that the gag order is necessary for national security or diplomatic relations. It is that final requirement — that courts can’t demand further explanation from the FBI — to which Judge Marrero devoted many of his objections in the 106-page decision.

“In many ways most troubling, this Court finds that the standard of review,” Judge Marrero wrote, “offends the fundamental constitutional principles of checks and balances and separation of powers.”

The plaintiff who brought the suit remains unidentified on the public docket. A statement by the American Civil Liberties Union, which represented the plaintiff, described the plaintiff as an Internet access company. The FBI has since dropped its request for information from the company.

“There is a tendency during periods of deep national anxiety, during periods of threats to national security, for the president and Congress to pursue national security goals even at the expense of civil liberties,” a lawyer with the New York Civil Liberties Union who was involved in the case, Arthur Eisenberg, said. Judge Marrero, who was nominated to the bench by President Clinton, wrote that the national security letter “serves as a critical tool to enable the government to perform investigations and law enforcement functions vital to the nation’s safety and security.”

However, there also existed strong reasons to allow public discussion about the information the government sought, Judge Marrero wrote.

The letters, Judge Marrero wrote, “can unmask the identity of Internet users engaged in anonymous speech in online discussions” and likely even be used to “discover the Web sites an individual has visited.”

“In light of the seriousness of the potential intrusion into the individual’s personal affairs and the significant possibility of a chilling effect on speech and association … a compelling need exists to ensure that the use of NSLs is subject to the safeguards of public accountability, checks and balances, and separation of powers that our Constitution proscribes,” the judge wrote.

In 2000, the year before the passage of the Patriot Act, the FBI issued 8,500 information requests in the form of national security letters. That number grew to 56,000 requests in 2004.

A spokesman for the Justice Department declined to comment about the ruling.

A bill, co-sponsored this year by a congressman from Manhattan, Rep. Jerrold Nadler, would require that the FBI have a higher level of cause before issuing such letters. It would also set a time limit for the gag order.

At the end of his 106-page decision, Judge Marrero grants a three-month stay before his order, which strikes down the FBI’s authority to issue national security letters, goes into effect.