SAN FRANCISCO — Usually it isn’t a good idea for a judge to look for supporting authority in a U.S. Supreme Court dissent.

Unless, of course, you’re a Clinton appointee on the Ninth Circuit U.S. Court of Appeals, you’re taking a controversial stand against the government on the state secrets privilege — and the guy you’re citing is Justice Antonin Scalia.

Ninth Circuit Judge Michael Daly Hawkins delivered an unqualified rebuke to the Obama administration on Tuesday in its bid to quash a civil suit brought by targets of the CIA’s extraordinary rendition program. The plaintiffs accuse Boeing subsidiary Jeppesen DataPlan Inc. of flying them to countries where they’d be tortured. President Bush, and then Obama, argued that the suit must be immediately dismissed because it involved state secrets.

Hawkins, however, found that the judiciary must have a role in reviewing secret executive branch conduct.

“As the Founders of this nation knew well, arbitrary imprisonment and torture under any circumstance is a ‘gross and notorious … act of despotism,’” Hawkins wrote, citing Scalia’s dissent in Hamdi v. Rumsfeld , in which the arch-conservative urged the court to go even further in protecting individual liberty against executive power.

Drawing more from Scalia, who in turn was quoting Blackstone, Hawkins wrote: “But ‘confinement [and abuse] of the person, by secretly hurrying him to [prison], where his sufferings are unknown or forgotten, is a less public, a less striking, and therefore a more dangerous engine of arbitrary government.’”

Judge Mary Schroeder and Senior Judge William Canby Jr., both Carter appointees, joined Hawkins.

Jeppesen’s attorney, Munger, Tolles & Olson partner Daniel Collins, did not return a call for comment. Plaintiff attorney Ben Wizner of the American Civil Liberties Union Foundation in New York City — and a former clerk for Judge Stephen Reinhardt — was ebullient. He tried to frame the decision as a nonpartisan one.

“I don’t think Hawkins is writing a liberal opinion. He’s writing an opinion that not just points the way for courts, but for the Obama administration as well,” Wizner said. “The Obama administration should be grateful for this opinion.”

A Justice Department spokesman said the government is reviewing the ruling.

To win an en banc call, the government would in theory need to get votes from all 11 active Republican appointees plus three Clinton judges. Barring U.S. Supreme Court review, the case returns to Northern District Judge James Ware, who had originally dismissed it.

At the time, Ware said he found “solace” in the fact that his decision would be reviewed by a higher court. And indeed, Hawkins rejected Ware’s reasoning that the government merely saying litigation involves state secrets automatically defeats it.

“According to the government’s theory, the judiciary should effectively cordon off all secret government actions from judicial scrutiny, immunizing the CIA and its partners from the demands and limits of the law,” Hawkins wrote.

Instead, the Ninth Circuit judge instructed Ware to scrutinize pieces of evidence so as to make an individual determination as to what is secret and can be withheld. If the plaintiffs then can’t make their case without excluded evidence — or Jeppesen is robbed of an affirmative defense — then the suit could still fail, Hawkins wrote in Mohamed v. Jeppesen DataPlan, 09 C.D.O.S. 5118 .

Jeppesen could also file its own motions to dismiss on other grounds, Wizner said, which could similarly head off discovery. Or it could settle, he said.

“This restores the state secrets privilege to its origin as a rule of evidence, not an immunity doctrine,” Wizner said.