A hazardous materials worker is hosed down on Capitol Hill in October 2001. The mailing of anthrax-laced letters that fall gave momentum to the idea that the military needed defenses against biological threats. (Ron Thomas / Associated Press / October 23, 2001)
 
Construction began in late October on a plant in north Florida that will produce flu vaccine and specialized medicines for the Pentagon to protect military personnel against germ warfare agents.

To begin paying for the initiative, the Obama administration has quietly shifted millions of dollars that had been budgeted for better masks, boots, early-warning sensors and other equipment for troops at risk of exposure to chemical or biological weapons, according to government documents and defense specialists.

The Department of Health and Human Services, meanwhile, is on track to spend billions of dollars to produce the same types of medicines in collaboration with private drug companies and university researchers.

The overlapping efforts are precisely what some policymakers have warned against. The Defense Department program also flies in the face of an analysis, commissioned by the White House, that examined ways the government could bolster production of vaccines and biodefense drugs.

The 2009 analysis recommended against establishing a government-controlled facility, akin to what the Pentagon is doing, saying that contracting with private manufacturers would produce new drugs more quickly and at a lower cost.

The 112-page report has not been shared with Congress or previously publicized. A copy of the document was obtained by the Los Angeles Times.

The Pentagon initiative has been championed by Assistant Secretary of Defense Andrew C. Weber, a presidential appointee. The Times' request for comment from Weber was referred to a top aide, James B. Petro.

In an interview, Petro said the Florida facility was needed to make medicines that the military could not rely on Health and Human Services or others to provide. The goal, he said, was to do "a more efficient and effective job" of acquiring the products.

"It's about making sure that our men and women in uniform have the protection that they need against these threats," said Petro, adding that Weber was aware of the 2009 analysis and that it had informed his staff's "strategic thinking."

Shifting funds from protective gear to help pay for the manufacturing effort was a "portfolio management decision" intended to "achieve balance in yielding both medical and physical defense equipment," Petro said.

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For decades, the government has contracted with outside companies for nearly all the medicines intended to protect the public and military personnel against infectious diseases. But the Defense Department has long sought to create its own medical manufacturing arm.

After the 1991 Persian Gulf War, the Pentagon spent hundreds of millions of dollars trying to develop vaccines against more than a dozen exotic pathogens, such as plague and the Ebola virus. The efforts ultimately fell short or were abandoned because of the costs and steep scientific challenges.

"This is a really, really hard thing to do," said David L. Danley, a biologist and retired Army colonel who supervised the Pentagon's vaccine-acquisition program. "The numbers — the costs — just didn't make sense."

The Defense Department has protected its battlefield personnel against the highest-profile biological threats — anthrax and smallpox — by securing access to Health and Human Services' stockpile of vaccines purchased from private pharmaceutical companies.

After the Sept. 11 terrorist attacks and the mailings of anthrax-laced letters that fall, the idea that the military needed defenses against a broader range of threats gained renewed momentum.

The Pentagon contracted with DynPort Vaccine Co. to develop biodefense vaccines, and by 2006 had paid the firm about $700 million. The work has not resulted in a product approved for use by the U.S. Food and Drug Administration.

In 2008, a report by researchers at the University of Pittsburgh Medical Center recommended that the Pentagon oversee the construction and operation of at least two plants for making biodefense medicines, saying that existing arrangements with private vaccine makers had yielded "limited success."

Army Maj. Gen. Stephen V. Reeves, then in charge of the military's defenses against biological and chemical warfare, publicly disagreed.