A federal judge has again halted the Pentagon’s mandatory anthrax vaccination program, declaring it illegal without the informed consent of service members or a presidential waiver of informed consent.

The ruling, handed down Wednesday by Judge Emmet Sullivan of the U.S. District Court for the District of Columbia, says the Food and Drug Administration failed to follow its own procedures in approving the vaccine as protection against anthrax used as a biological weapon.

As things stands now, he said, the vaccine is not properly approved for that specific purpose and as such is an investigational new drug.

“Unless and until” FDA properly classifies the vaccine as safe and effective for use against inhalation anthrax, Sullivan said, “the involuntary anthrax vaccination program, as applied to all persons, is rendered illegal absent informed consent or a presidential waiver.”

In 1980, an expert panel advising the FDA said the vaccine was safe and effective against anthrax in limited occupational settings, such as for industrial workers exposed to infected animal fur or hide. The panel also noted the vaccine was intended to protect only against anthrax contracted through the skin and said it could not determine if the vaccine would be effective against inhalation anthrax.

In 1985, the FDA unveiled a proposed rule on the use of the vaccine in such limited occupational settings. But it was not until December 2003 — five years after the military began its mandatory inoculation program — that the FDA issued a final rule stating that the vaccine also protects against inhalation anthrax.

However, Sullivan said that in the years since 1985, the FDA failed to provide a “meaningful opportunity” for public comment on its proposed rule regarding the vaccine, as required by its own regulations, Sullivan said.

“This failure … violates the Administrative Procedures Act,” and thus renders the vaccine’s use against inhalation anthrax illegal, Sullivan said.

This is the second time in less than a year that Sullivan ruled the vaccine was not properly licensed to protect against weaponized anthrax.

He first issued a temporary injunction to shut down the program in December. Just eight days later, the FDA came out with its final rule saying the vaccine was safe and effective protection against all forms of anthrax.

Noting the announcement came hard on the heels of his injunction and followed 18 years of inaction, Sullivan described the timing as “arguably highly suspicious.”

Nevertheless, he lifted his injunction while he considered the legality of the FDA’s final rule and related issues. His ruling Wednesday represents his decision on that question.

“It’s been a long fight … it’s not over yet, but right now we feel vindicated,” said attorney John J. “Lou” Michels Jr., one of the attorneys representing six anonymous service members and civilians subject to the military’s mandatory vaccination policy who sued the government.

Although the lawsuit focused on only six people, Sullivan said his injunction applies to everyone subject to the mandatory anthrax vaccination program.

Defense officials could not immediately be reached for comment. Michels said he expects the Pentagon to appeal the decision.

• Read Judge Sullivan’s decision in its entirety.