"We feel it is important to offer this short-term alternative to parents and health care providers in order to ensure young children are protected from the potentially severe effects of the flu," Kim Belshe, secretary of the California Health and Human Services Agency, said in a statement.
The exemption affects children under the age of 3 and will last six weeks, giving the manufacturer of the pediatric vaccine, Pennsylvania-based Sanofi Pasteur, time to ship about 500,000 more doses.
Although California has received only half the doses ordered, at least three local providers -- Kaiser Permanente, Stanford Hospital and the Santa Clara County health department -- said they have no shortage of either adult or pediatric vaccine.
But while Palo Alto Medical Foundation has plenty of shots for children, it has used up all its adult vaccine and is waiting for more. The foundation canceled clinics that had been scheduled through Nov. 12 at all five of its locations.
"We used essentially everything we had -- in fact we borrowed some from other local providers who had gotten their full shipments," said spokeswoman Jill Antonides.
Santa Clara County, on the other hand, is in good shape, with enough of both kinds of vaccines for patients until more doses arrive.
The preservative, called thimerosal, has been used in vaccines since the 1930s to prevent bacterial and fungal contamination. Tt is about 50 percent mercury by weight.
In the 1990s, some parents and pediatricians became concerned that thimerosal in children's vaccines might be connected to a nationwide surge in autism rates.
There is no scientific evidence linking thimerosal to childhood neurological diseases, said Dr. Randy Bergen, a pediatric infectious disease specialist at Kaiser Permanente.
He said that while he understands parents' concerns, "I would have no reservations about giving this vaccine to my kids, and didn't have reservations when they were that old."
However, a state law banning thimerosal from vaccines given to pregnant women and children younger than 3 took effect this year, backed by lobbying from groups that say mercury is linked to autism.
But the law can be waived when the pediatric vaccine is in short supply. That's what four groups -- the California branch of the American Academy of Pediatrics, California Medical Association, California Academy of Family Physicians and Kaiser Permanente -- asked the state to do.
Young children and the elderly are among those most vulnerable to serious, even fatal complications from influenza. And children under 3 who are getting their first flu shots actually need two doses one month apart for full, Bergen said.
J.B. Handley, a former Lafayette resident and the father of an autistic son, said state officials should launch an informational campaign to make sure parents know the flu shot their child receives may contain thimerosal.
"The state of California has an obligation to inform parents of this backward step that is re-introducing a neurotoxin to young children," Handley said.
However, Rick Rollens, father of an autistic child and a co-founder of the M.I.N.D. Institute at the University of California-Davis, supported the waiver so long as it is temporary.
"It took a lot of courage for the governor to sign this bill to begin with," Rollens said. "He had a tough decision to make on this issue and I think he has taken the right step."