U.S. District Court Judge Vaughn Walker said the plaintiffs provided enough evidence to show "they were subjected to warrantless electronic surveillance" by the National Security Agency.
The judge's 45-page ruling focused narrowly on the case involving the Al-Haramain Islamic Foundation, touching vaguely on the larger question of the program's legality.
Nonetheless, Al-Haramain lawyer Jon Eisenberg said the ruling had larger implications.
"By virtue of finding what the Bush administration did to our clients was illegal, he found that the Terrorist Surveillance Program was unlawful," Eisenberg said.
President Bush authorized the surveillance program shortly after 9/11, allowing NSA officials to bypass the courts and intercept electronic communications believed connected to al-Qaida.
Generally, government investigators are required to obtain search warrants signed by judges to eavesdrop on domestic phone calls, e-mail traffic and other electronic communications.
At issue Wednesday was a 2006 lawsuit filed by the Ashland, Ore., branch of the Saudi-based foundation and two American lawyers Wendell Belew and Asim Ghafoor.
Belew and Ghafoor claimed their 2004 phone conversations with foundation official Soliman al-Buthi were wiretapped without warrants soon after the Treasury Department had declared the Oregon branch a supporter of terrorism. They argued that wiretaps installed without a judge's authorization are illegal.
It was the last active case pending before a trial judge challenging the wiretapping program that ended in 2007.
"The ruling ends the case, but without the fireworks everyone expected," George Washington University law professor Orin Kerr said. "It ended with a whimper."
The plaintiffs were seeking $1 million each, plus attorney fees in the case. Walker ordered more legal arguments before deciding on possible damages.
The ruling came after U.S. Attorney General Eric Holder said the lawsuit threatened to expose ongoing intelligence work and must be thrown out.
In making the argument, the Obama administration agreed with the Bush administration's position on the case but insisted it came to the decision differently.
Holder's effort to stop the lawsuit marked the first time the administration has tried to invoke the state secrets privilege. Under the strategy, the government can have a lawsuit dismissed if hearing the case would jeopardize national security.
Holder said Judge Walker had been given a classified description of why the case must be dismissed so the court could "conduct its own independent assessment of our claim."
That was a departure from the Bush administration, which resisted providing specifics to judges handling such cases about what the national security concerns were.
Holder previously said the administration would respect the outcome of Walker's review.
Eisenberg called on the Obama administration to accept Wednesday's ruling and forgo any appeals.
"We are reviewing it," Department of Justice spokeswoman Tracy Schmaler said.
In June, Judge Walker tossed out more than three dozen lawsuits against the nation's telecommunications companies for allegedly taking part in the program.
Congress in 2008 agreed on new surveillance rules that included protection from legal liability for telecommunications companies that allegedly helped the U.S. spy on Americans without warrants.
Walker previously upheld the constitutionality of the new surveillance rules. His ruling is being appealed.
Anthony Coppolino, the U.S. Department of Justice lawyer who has been in charge of the Islamic Foundation case under both administrations, has never addressed the legality of the wiretap program.
Coppolino has always argued the case should be tossed out in the name of national security and said the government risked exposing ongoing intelligence work if the lawsuit were allowed to proceed.
The government argued that its "state secret privilege" trumped the Foreign Intelligence Surveillance Act, known as FISA, which requires investigators to seek wiretap approval from a special court that convenes behind closed doors.
Coppolino refused to even discuss whether such a secret warrant existed, arguing that to confirm or deny would threaten national security.
On Wednesday, the judge said the government was wrong and ruled that it should be assumed investigators lacked a warrant.
"FISA takes precedence over the state secrets privilege in this case," Walker wrote.
The Bush administration invoked the secrets privilege numerous times in lawsuits over various post-9/11 programs.
In another wiretap case targeting the Bush tactics, the Center for Constitutional Rights asked the U.S. Supreme Court Tuesday to order government officials to disclose if officials eavesdropped without warrants on electronic conversations between 23 attorneys and their clients held at Guantanamo.
Lower courts had tossed out that request.
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