Despite months of dire warnings and millions in taxpayer dollars, less than half of the 229 million doses of H1N1 vaccine that the government bought to fight the pandemic have been administered. That means an estimated 71.5 million doses must be discarded if they are not used before they expire.

Between 81 million and 91 million doses of swine flu vaccine were injected into peoples’ arms or squirted up their noses through the end of February, according to federal officials, leaving about 138 million doses unused. An estimated 60 million of those will be donated to poor countries or saved for possible future use. But doses already in vials and syringes will be thrown away if not used before their expiration dates pass.

The prospect of millions of doses of the once-precious vaccine being discarded is the latest twist in the $1.6 billion program, the most ambitious immunization campaign in U.S. history. The government-led effort produced a vaccine in record time, but unexpected production problems delayed delivery of the bulk of supplies until after the second wave of infections had peaked, leaving millions anxious and frustrated as they scrambled for the shots and nasal sprays.

Nevertheless, officials said they were largely satisfied with the effort, which blunted the impact of the first flu pandemic in decades. Between 72 million and 81 million people are estimated to have been immunized.

“Did we do as well as we would have liked to? No, not at all,” said Anne Schuchat of the federal Centers for Disease Control and Prevention. “But the country did an extraordinary job of responding. It’s pretty incredible to think about how much uncertainty we had at the beginning of this.”

Given the potential seriousness of the threat and the uncertainties of vaccine production, Schuchat said, it was unavoidable that some doses would go to waste.

“We were dealing with a very unusual situation. We had a pandemic. We had young people being killed,” she said. “We wanted to make sure we had enough. We didn’t want to be short. It was important to us to be able to protect the American people.”

Noting that the virus still poses a threat, Schuchat and other experts stressed that they hope millions more in the country will still get vaccinated.

“It’s too early to write the final chapter on this vaccine,” said Michael Osterholm of the University of Minnesota. “If we’re at the beginning of a third wave, I just bet you a lot of that vaccine that is sitting there will not be unused.”

But officials acknowledge that it becomes more difficult in spring to persuade a skeptical public to get vaccinated, especially because the threat appears to be fading.

“We still don’t know what the future is. We need to be nimble enough in case there is an uptick in disease,” said Bruce Gellin, head of the National Vaccine Program Office.

The immunization program was designed to provide enough vaccine to protect every U.S. resident if needed. But antiquated technology dependent on growing the virus in chicken eggs delayed arrival of most of the doses. Fears about the pandemic fostered wide-scale anxiety and spawned long lines as the first doses trickled in amid the second wave of infections last fall. the time the vaccine was plentiful, demand had dissipated.

Of the 229 million doses bought by the federal government, about 162.5 million were put into vials and syringes, which starts the clock ticking on an expiration date.

About 25 million are being donated to poor countries, and about 35 million remain in bulk form, which lasts longer and could be used if the virus flares up again later this year or as part of next year’s seasonal flu vaccine. The Defense Department received about 3 million doses.

More than 900,000 doses of H1N1 vaccine were still available in Maine in early February.

Overall, about one-third of people considered at the highest risk from the virus, including nearly 37 percent of children ages 6 months to 17 years, were vaccinated through January. But the proportion of people immunized varied widely nationwide, with some states reporting vaccination rates three times as high as others.

“The message we should take away from this experience is that we need to continue to explore technologies to improve the stability of the flu vaccine supply and, equally as important, we need to invest in public health infrastructure to make sure that there are strong health departments to communicate with the public and administer vaccine once it is produced,” said Rep. Henry Waxman, D-Calif..

The World Health Organization, meanwhile, faces mounting charges that it overreacted to the pandemic. The Council of Europe’s Parliamentary Assembly is investigating allegations that the Geneva-based arm of the U.N. was influenced by pharmaceutical companies to exaggerate the risk, accelerating vaccine sales.

WHO officials have strongly disputed the charges, saying the response was vital given the uncertainty about the new virus and its potential threat. Many independent public health experts have defended the agency.

Nevertheless, the WHO has launched an internal review of its response. It announced Monday that a committee of 29 outside experts would conduct an independent assessment.