ARLINGTON, Va. — In an about-face decision, the Pentagon has stopped vaccinating troops against anthrax, halting the program and the quandary of what to do with troops who refuse to get the anthrax vaccine.

A ruling by a federal judge Monday surprised defense officials and led to some confusion as they tried to figure out how to handle the imposed temporary injunction.

David Chu, under secretary of defense for personnel and readiness, notified service secretaries and other leaders in a one-paragraph memorandum that “[p]ending further notice, the Deputy Secretary has decided that DOD will stop giving anthrax vaccinations until the legal situation is clarified.”

In spite of sharp criticism from troops who have said the vaccine made them ill, Pentagon leaders have lauded the vaccine as extremely safe — and deem it critical in protecting the lives of U.S. forces deployed to high risk areas of the world where the weaponized deadly bacteria can be used against them.

Because Friday was a federal holiday, no officials were available to speak on the reversed policy decision, and the possible impact as troops continue to be deployed.

Chu’s memo countered the message delivered earlier Tuesday by Pentagon officials who said the program would continue for troops who had no objection to getting the controversial vaccine. Officials did not know Tuesday what would happen, if anything, to servicemen and women who refused to be vaccinated. For years, the Pentagon has taken disciplinary action against troops who defied the military order — discharging and even jailing some.

Such was the confusion earlier this week among the Pentagon’s leadership that Dr. William Winkenwerder Jr., assistant secretary of defense for health affairs, stood behind the Pentagon’s lectern Tuesday afternoon and refused to say whether the department planned to obey the judge’s order.

“So, in other words ... you won’t say right now whether or not the Department of Defense is complying with a federal court order? That’s your answer to us,” asked a defense reporter.

“That’s correct,” Winkenwerder responded. “There is interpretation of what that order means. That’s a process that we need to review, that we are reviewing, that our attorneys are reviewing. And we’ll have an answer as soon as practicable.”

Following the briefing, other officials scurried to retract the message. “Of course we’re going to comply with the order,” said one defense official. “The Defense Department does not go around breaking the law.”

U.S. District Judge Emmet G. Sullivan ruled the vaccine was approved by the Food and Drug Administration to protect against the skin form and not against inhaled anthrax. The ruling states that using the vaccine to protect against inhaled anthrax makes is an experimental drug, and forcing troops to take the shot therefore violates the law.

Pentagon leaders disagreed with the finding, saying the FDA approved the vaccine in 1970 for all forms of anthrax.

“A clarification on that, on their [FDA] part, is something that we’ll need,” Winkenwerder said.

Lawyers will continue to argue the case before Sullivan in a March hearing in his chambers.

The judge’s ruling, however, could be voided if President Bush decides to issue a special presidential waiver of troops’ right to informed consent, typically used for experimental, trial and clinical drugs. The Pentagon asserts the vaccine is none of those.

“Looking forward, the president can basically terminate the entire controversy by just granting the waiver,” said Eugene Fidell, president of the National Institute of Military Justice and a military law expert. “The president has power to grant the waiver, but … he must be accountable for that decision to terminate a controversial program.”

Roughly one million U.S. troops have received the vaccine since 1998. Between then and 2001, about 400 troops had refused to be vaccinated. Since June 2002, when the supply shortage was remedied, only 10 have refused, Winkenwerder said.

The ruling, however temporary, could spell out other long-term legal implications for troops who faced or still face disciplinary action for refusing to consent to receiving the vaccine, Fidell said.

But the road ahead still is speculative, he said.

Those who received a bad discharges or disciplinary notes in their records might seek appeals to review boards to have statuses reversed.

“No agency looks for things to apologize for, and I wouldn’t hold my breath for an apology in this area,” Fidell said.

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