A federal judge on Wednesday permitted the U.S. Defense Department to begin giving troops anthrax vaccinations on a voluntary basis after ordering a halt last October to mandatory shots.

U.S. District Court Judge Emmet Sullivan granted the Bush administration’s request to modify last fall’s injunction to allow for voluntary inoculations under a 2004 law bolstering the government’s ability to protect against bioterrorism.

Sullivan on Oct. 27 forbade the Pentagon from giving the anthrax shots to military personnel, stating that the Food and Drug Administration had acted improperly when it allowed the experimental shots for general use.

The Pentagon had given the shots to 1.2 million troops since 1998.

Anthrax spores can be used in germ warfare to give victims the deadly bacterial disease.

Lt. Col. Chris Conway, a Pentagon spokesman, called the anthrax vaccine “an important force protection measure,” but said the vaccines will not be offered until the department completes detailed rules “in the near future.” Conway was not more specific on the timetable.

Sullivan’s action came in a lawsuit filed by six unnamed military personnel and civilian workers who objected to the vaccinations. A relatively small number of U.S. troops have refused to get the Pentagon’s mandatory anthrax and smallpox shots due to worries about side effects, and some have been thrown out of the military.

In his order, Sullivan wrote that with the 2004 law “Congress appears to have authorized the use of unapproved drugs or the unapproved use of approved drugs based on a declaration of emergency by the secretary of health and human services.”

Sullivan wrote that the law said such a declaration would be based on a determination by the defense secretary of the existence of or potential for a military emergency in which U.S. forces faced the threat of attack with chemical, biological, radiological or nuclear weapons.

The Pentagon had mandated that many troops deployed to Iraq and Afghanistan get the anthrax shot, and widened its anthrax vaccinations last summer to include personnel in South Korea.

Pentagon officials have insisted the shots are safe and effective.

But the lawsuit contended that the drug was never shown to protect against the form of anthrax in which airborne bacterial spores are inhaled into the lungs - the most likely way troops would face the disease on a battlefield.

Sullivan ruled in 2003 the FDA had never approved the vaccine and issued an order halting Pentagon vaccinations. The next week, the FDA approved the vaccine, and the shots were resumed only to be halted again last October.