A federal appeals court in San Francisco on Wednesday threw out a lawsuit seeking to hold a government contractor partly responsible for a secret CIA program to whisk terror suspects to undisclosed prisons overseas for brutal interrogations.

The Ninth US Circuit Court of Appeals voted 6 to 5 to dismiss the lawsuit filed on behalf of five individuals who charged they were seized and imprisoned without legal process, and tortured at the behest of the Central Intelligence Agency.

The appeals court action ends the litigation before it was able to formally begin. The majority judges said they felt compelled to throw the suit out under legal precedents upholding the so-called state secrets doctrine.

The plaintiffs sued Jeppesen Dataplan, a Boeing subsidiary, that allegedly provided air transport and other international logistical support to the CIA operation. The CIA program, known as “extraordinary rendition,” was instituted during the Bush administration and has continued with some changes under President Obama.

Although the executive branch won in court, the majority judges were troubled by their ruling.

“After much deliberation, we reluctantly conclude … the plaintiff’s action must be dismissed,” wrote Judge Raymond Fisher.

The plaintiffs’ lawyer, Ben Wizner of the American Civil Liberties Union, said it was a sad day. He pledged to appeal to the US Supreme Court.

“To date, not a single victim of the Bush administration’s torture program has had his day in court,” Mr. Wizner said in a statement. “If today’s decision is allowed to stand, the United States will have closed its courtroom doors to torture victims while providing complete immunity to their torturers.”

Richard Samp, a lawyer with the conservative Washington Legal Foundation, praised the decision.

“The judicial branch is simply not the appropriate forum for airing these types of issues,” he said in a statement. “The CIA could not maintain the confidentiality of its affairs if those who oppose its policies were free to air their opposition in an open courtroom.”

Under the state secrets doctrine, courts have generally granted deference to executive branch claims that certain litigation may involve highly sensitive US government information which, if disclosed, would cause significant damage to national security.

The Bush administration argued that Mohamed v. Jeppesen was just such a case. The Obama administration continued with that argument.

The majority judges said because of state secrets concerns they were precluded from explaining in detail why the case could not move forward without harming national security. But they said they were convinced such harm would result.

“Any effort by Jeppesen to defend [against the suit] would unjustifiably risk disclosure of state secrets,” Judge Fisher wrote.

In a dissent joined by four other judges, Judge Michael Hawkins said the court was wrong to dismiss the entire lawsuit at such an early stage. He said the case should be remanded to a federal judge to determine to what extent actual evidence in the case might raise a threat of disclosing state secrets.

Hawkins acknowledged that the state secrets doctrine is an established precedent. But he said the privilege need not be so broadly enforced.

“The doctrine is so dangerous as a means of hiding governmental misbehavior under the guise of national security, and so violative of common rights of due process, that courts should confine its application to the narrowest circumstances that still protect the government’s essential secrets,” he wrote.

The majority concluded its opinion with a quasi apology to the plaintiffs. “Our holding today is not intended to foreclose – or to prejudge – possible nonjudicial relief, should it be warranted for any of the plaintiffs,” Judge Fisher said.

He said in the interest of justice the government might examine the plaintiffs’ claims and – if warranted – award reparations to them. In addition, he suggested there might be a Congressional investigation and remedial action by lawmakers.

“It should be a rare case when the state secrets doctrine leads to dismissal at the outset of a case,” Fisher wrote. “This is one of those rare cases.”

Judge Hawkins countered in his dissent that the majority’s suggested alternative remedies undercut the concept of checks and balances. “Permitting the executive to police its own errors and determine the remedy dispensed would not only deprive the judiciary of its role,” he said, “but also deprive the plaintiffs of a fair assessment of their claims by a neutral arbiter.”