Crumbling rubber stoppers on vials are letting in moisture, and a brilliant green dye is inexplicably losing its color, but the vaccine remains near normal potency, Federal experts say. The bigger problem is that the American supply of a colorless liquid medicine, known as vaccinia immune globulin, which is needed to counteract adverse reactions to the vaccine, has turned pink for reasons no one understands. Federal rules say the medicine must be on hand before vaccinations are given, and the Food and Drug Administration has barred its use until the mystery is solved.

A further complication is that new batches of vaccine cannot be made with the old process, since today that process would fail to pass the F.D.A.'s more rigorous standards.

In late 1997, prompted in part by Mr. Alibek's revelations, the Pentagon embarked on a $322 million program to make new vaccines for the military, including smallpox. The earliest it will be ready, officials say, is 2005 -- if it can pass F.D.A. muster. That will be difficult. Because the disease no longer exists and the virus is too lethal to unleash on people, clinical trials cannot be conducted to test whether or not the new vaccine actually helps humans resist smallpox.

''Ultimately, they're going to have to make a fairly substantial judgment call,'' Steve Pryor, president of Dynport, the Pentagon's vaccine contractor, said of F.D.A. officials.

Civil authorities in Washington want at least 40 million doses of new smallpox vaccine, and health experts like Dr. Henderson, who now heads a center for the study of bioterrorism at Johns Hopkins, are calling for 100 million. Talks are under way for Dynport to produce vaccine for civilian use as well, but nothing to date has been worked out.

Meanwhile, some experts question the whole vaccine approach as a germ warfare safeguard. Foes, they say, knowing well in advance about vaccinations, might counter them by switching to a different germ or a different variant, perhaps genetically engineered.

''Defensive measures are much more difficult than offensive ones,'' said William C. Patrick 3d, who made germ weapons for the United States before President Nixon outlawed them three decades ago.