Autism advocates are set to protest tomorrow against a quiet effort by Mayor Michael Bloomberg’s administration to require annual flu vaccinations for all New York City schoolchildren under 5 years of age.

On Wednesday, with just three weeks to go until he leaves office, Mr. Bloomberg’s controversial Board of Health is set to vote on new rules that would force children as young as six months old to be immunized each year before December 31 if they attend licensed day care or pre-school programs.

“Young children have a high risk of developing severe complications from influenza. One-third of children under five in New York City do not receive an annual influenza vaccination, even though the vaccine safely and effectively protects them against influenza illness,” the Health Department said in a statement. “This mandate will help protect the health of young children, while reducing the spread of influenza in New York City.”

The Board’s members are all mayoral appointees and controversial initiatives–from smoking bans to regulations on soda cup sizes–have historically sailed through with little opposition, angering a small, but vocal group of advocates who claim the vaccinations are potentially dangerous.

“The Bloomberg administration is wildly exaggerating the benefit of the flu shot and we think they are wildly underestimating the risks involved with it,” said John Gilmore, the executive director of the Autism Action Network, speaking more broadly than the controversial claim that links vaccines to autism.

“There are risks associated with every medical procedure,” he said, citing allergic reactions, toxic mercury used as a preservative and questions as to whether the Board’s move is legal given state government jurisdictions.

Mr. Gilmore’s organization is helping organize tomorrow’s protest. And though he doesn’t expect the Board’s vote to go his way, he hopes the rally will get Mayor-elect Bill de Blasio’s attention, potentially opening the door for a reversal once he takes office in January.

“This is basically to put the mayor-elect [on alert], make him aware that this is an issue that he’s going to have to deal with it. It’s not going to go away,” said Mr. Gilmore said, criticizing the way the Bloomberg administration has pushed the rules through. “He is kind of doing this in a stealth fashion. He just proposed this about 6 weeks ago. I don’t think there was any announcement.”

According to a Board of Health notice made public in September, influenza results in 20,000 hospitalizations and 30 to 150 deaths in children under 5 nation-wide each year.

Under the proposed rule, which had a public hearing in October, the vaccinations would be required “unless the vaccine may be detrimental to the child’s health, as certified by a physician licensed to practice medicine in this state, or the parent, parents, or guardian of a child hold genuine and sincere religious beliefs which are contrary to the practices herein required.”