"Cases engendering intense passions and urgencies to unencumber the Government," Judge Marrero wrote, "enabling it to move in secrecy to a given end with the most expedient dispatch and versatile means, often pose the gravest perils to personal liberties."
The decision is the second time a judge has ruled unconstitutional part of the Patriot Act, a package of prosecution and surveillance tools passed shortly after the terrorism of Sept. 11, 2001.
In January, a federal judge in Los Angeles struck down a section of the act that made it a crime to give "expert advice or assistance" to groups designated foreign terrorist organizations. The judge said the language was too vague, threatening First and Fourth Amendment rights.
American Civil Liberties Union attorney Jameel Jaffer called the latest ruling a "landmark victory, and "a wholesale refutation of excessive government secrecy and unchecked executive power."
Marrero said his ruling blocks the government from issuing new requests for phone and Internet records "in this or any other case," but delayed the injunction by 90 days to allow time for an appeal.
The judge said the law violates the Fourth Amendment because it bars or deters any judicial challenge to the government searches, and violates the First Amendment because its permanent ban on disclosure is a prior restraint on speech.
He noted that the Supreme Court recently said that a "state of war is not a blank check for the president when it comes to the rights of the nation's citizens."
"Sometimes a right, once extinguished, may be gone for good," Marrero wrote.
Marrero issued his decision in favor of an Internet access firm identified in his 120-page ruling simply as "John Doe." He had agreed to keep the firm's identity secret to protect the FBI probe that led to the search request.
President Bush has been pushing Congress to renew all of the Patriot Act before it expires next year, arguing that it is one of law enforcement's best tools in preventing another catastrophic terrorist attack.
The law has become a symbol to civil libertarians who say the Bush administration has gone too far in expanding security powers at the expense of privacy rights and individual freedom.
In a footnote to his ruling, Marrero cited words he had written two years ago in another case to warn that courts must apply "particular vigilance to safeguard against excess committed in the name of expediency."
"The Sept. 11 cases will challenge the judiciary to do Sept. 11 justice, to rise to the moment with wisdom equal to the task, its judgments worthy of the large dimensions that define the best Sept. 11 brought out of the rest of American society."