ARLINGTON, Va. — The Pentagon isn’t sure how it will deal with troops who refuse to get the anthrax vaccine now that a federal judge has temporarily banned the Defense Department’s policy that it be mandatory.

“We are considering all options,” said William Winkenwerder Jr., assistant secretary of defense for health affairs, adding he did not know if troops would continue to face punishment if they refuse the vaccine.

While officials work it out, the Pentagon still is administering anthrax vaccines to troops deploying to high-risk areas, but on a voluntary basis.

U.S. District Court Judge Emmet G. Sullivan’s ruling on Monday “came quite as a surprise,” Winkenwerder said.

“There is some interpretation as to what the order means,” Winkenwerder said. According to Sullivan’s ruling, short of a presidential special order, the Pentagon cannot force troops to get the vaccine.

Sullivan ruled the vaccine is not approved by the Food and Drug Administration for use against inhalation anthrax, and as such, is an experimental drug.

But Winkenwerder disagreed with the finding, saying the vaccine was approved by the FDA in 1970 for all forms of anthrax, and “a clarification by the FDA on their part is what we need,” Winkenwerder said. Lawyers will continue to argue the case before Sullivan in a March hearing in his chambers.

“The decision is not supported by medical science or medical fact,” Winkenwerder said.

Defense Secretary Donald Rumsfeld said it was too premature to speculate on how the judge’s order would change, if at all, the Pentagon’s policy to vaccinate all servicemembers who travel to high-risk areas.

“The decision is recent and the lawyers are examining it. At the appropriate time, we’ll be making a recommendation as to the way forward,” Defense Secretary Donald Rumsfeld said Wednesday during a press briefing. “I don’t want to comment on any specifics.”

Both Winkenwerder and Rumsfeld strongly objected to Sullivan’s characterization that the Defense Department was using personnel “as guinea pigs for experimental drugs.”

“Obviously, that comment, if he said it, is inaccurate,” Rumsfeld said.

“I categorically reject use of that term with response to the treatment of our servicemembers,” Winkenwerder said.

Air Force Gen. Richard Myers, chairman of the Joint Chiefs of Staff, said the vaccine not only is safe, but also needed to protect troops sent into harm’s way.

Since the program’s inception, roughly 1 million servicemembers have been vaccinated. Since June 2002, the number varies between 600,000 and 700,000, Winkenwerder said. Of those recent vaccinations, the Pentagon has seen about 10 refusals, dramatically lower from the roughly 400 between 1998 and 2001, he said.

Anthrax is a deadly biological agent that can be weaponized.

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