A federal judge on Wednesday barred the U.S. military from forcing troops to be vaccinated for anthrax without either getting their informed consent or obtaining a special order from President Bush.

About 1 million troops have already been given the shots in the six-year-old program and many who refused have faced punishment, including being thrown out of the military.

U.S. District Judge Emmet Sullivan set aside a final rule and order by the Food and Drug Administration that late last year declared the anthrax vaccine safe and effective to protect troops against inhaled exposure of the deadly bacteria.

“By refusing to give the American public an opportunity to submit meaningful comments on the anthrax vaccine’s classification, the agency violated the Administrative Procedures Act,” he ruled in a 41-page decision.

Defense officials have said about 1 million troops have been given the shots under the anthrax vaccination program. Some have reported inflammation in the area of the vaccination. Others have reported extreme fatigue, joint pain and temporary memory loss.

Worried about possible dangerous side effects, hundreds of U.S. service members have refused the vaccinations and many have been punishment, including being discharged.

Sullivan told the Food and Drug Administration to reconsider the issue after an appropriate public comment period. In the meantime, he barred the military from continuing the compulsory vaccinations.

“Congress has prohibited the administration of investigational drugs to service members without their consent. This court will not permit the government to circumvent this requirement,” he wrote.

“The men and women of our armed forces deserve the assurance that the vaccines our government compels them to take into their bodies has been tested by the greatest scrutiny of all - public scrutiny,” Sullivan said.

The ruling came in a lawsuit brought by six unidentified troops and civilian workers for the Department of Defense who challenged the military’s policy.

Mark Zaid, a lawyer for the six plaintiffs, hailed the ruling. “We’re ecstatic. This confirms that we’ve been stating for six years now - that the program was illegal and ill-conceived from day one.”

The Defense Department said it remained convinced that the vaccine is safe but would stop giving anthrax vaccinations until the legal situation was clarified.

Anthrax is considered the No. 1 biological weapon threat. It can be transmitted in three ways - through inhalation of the spores, into a cut in the skin, or by eating contaminated meat.

Inhaled anthrax is by far the deadliest form. In 2001, five Americans died from anthrax inhaled from contaminated mail.

The Justice Department is reviewing the ruling, a spokesman said.