New Haven school children may not be able to avoid a flu shot this year.

Amid flu season and the increased threat of the H1N1 virus, city health officials are confronting the question of how to allocate government-issued vaccinations, which Gov. M. Jodi Rell announced will arrive in the state in mid-October. State officials have released vaccination plans to protect groups most at risk for both seasonal flu and H1N1, but some New Haven officials said they are still waiting for more information about distribution — and about the vaccines themselves — before they act.

William Quinn, the director of the New Haven Department of Health, said he and other officials are currently expecting many cases of both H1N1 and seasonal flu. Schoolchildren — one of what he calls the “special populations” at risk — are the utmost priority for vaccinations, he said. In the spring, 300 children had contracted H1N1, and this fall’s onset of the disease may disproportionately hit similarly vulnerable groups.

“It’s very dangerous for these kids,” he said. “Right now we’re asking all physicians to give us a hand with vaccinating everyone.”

Quinn said all children should receive the H1N1 vaccine directly from either their primary care physicians or the city’s school-based health clinics. He said that because physicians know their patients better, doctors rather than schools should be the primary distributor of the vaccines.

“Right now, we prefer physicians,” Quinn said. “Someone who knows the student, knows his medical history, knows the best course of action.”

But as many local officials prepare for the potential of a wider outbreak, additional consideration must be given as to the most efficient allocation method. Carlos Ceballos, director of New Haven’s school-based health clinics, said vaccinations administered directly in schools may be a better way to ensure universal protection. His clinics, which he said may be a more accessible resource, serve as the de facto personal physician for many of the city’s schoolchildren.

“School vaccinations allow us to make sure we’ve gotten all the kids,” he said. “They’re easier to track in school. With primary physicians, that’s a lot of doctor’s notes.”

Quinn conceded that final decisions must be delayed until the city knows how many physicians sign up to help. When asked whether schools could be used for distribution, he said he would not dismiss the option, adding that his department could consider schools “if need be.”

Gov. M. Jodi Rell announced Sept. 9 that 45 million doses of H1N1 vaccine would be made available to municipalities throughout the state, and though she said there will be enough to meet demand, the ultimate number of doses allocated will depend on the size of the city’s at-risk populations. She said Connecticut will receive a shipment of 500,000 doses of the H1N1 vaccine from the federal government, with an additional 200,000 doses each week.

Ceballos explained that seasonal flu vaccinations for all students will continue to be available through private physicians and clinics. Potentially, he said, students may have to receive the seasonal flu vaccine from doctors and the H1N1 vaccine directly from schools.

The Health Department and clinics are coordinating with regional health planners and the federal Centers for Disease Control to implement the vaccination regime.