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Authorities were caught short by swine flu, he said, because it appeared in Mexico in April, about the end of the normal flu season.

“Right from the get-go we were three months behind,” Dr. Fauci admitted.

More investment is needed in next-generation technology, because the “tried and true” method of growing vaccines in eggs is too slow, especially in the case of H1N1, and has too much variability, he said.

That will require the government to offer industry some incentives, because there are too many uncertainties in the vaccine business for the private sector to invest enough on its own, he said.

The government partially funded a Novartis plant in North Carolina with $487 million in January, before swine flu was identified. The Swiss company’s plant is not yet operational, but would use a new cell-based technology that is reportedly more predictable and controllable and produces vaccines faster.

“But the real endgame is to bring the technology into the 21st century and use molecular biological techniques so that you can really have control about making the purified proteins that you want,” Dr. Fauci said.

“What we’re faced with is the need to partner with companies so that we can essentially assume some of the expenses of making the transition from egg to cell and then ultimately the basic research, which is what we do, which takes years, to go into the avant-garde technology,” he said.