A law banning a mercury-based preservative called thimerosal from vaccines given to pregnant women and children under three took effect this year, backed by health groups who claim that mercury is linked to autism.
However, only one manufacturer, Sanofi Pasteur, the vaccine unit of French drug giant Sanofi-Aventis, produces the vaccine that complies with California's law, and this year, it started shipping its vaccines three weeks later than usual.
The vaccine manufacturer blamed the delay on difficulty making the vaccine, as flu strains change every year and one of the new strains grew slower than normal, holding up the manufacturing process.
Pressured by physicians from four medical groups, HHS secretary Kim Belshe agreed to a six-week waiver of the ban because she says the health threat from flu outweighs the worries about mercury-free vaccines.
The medical groups said the delays in vaccine production meant that paediatricians have received only partial orders of mercury-free flu vaccines and were having to turn away patients, meaning that many young children could not be protected during the flu season.
However, many doctors have flu shots available with thimerosal that can be used now that the ban is suspended.
Meanwhile, the exemption will also give Sanofi Pasteur time to ship about 500,000 doses of the vaccine without the preservative.
Thimerosal is a mercury-containing preservative used in some vaccines and other products since the 1930s.
According to the Institute of Medicine, no harmful effects have been reported from thimerosal at doses used in vaccines, except for minor reactions like redness and swelling at the injection site, and no scientific evidence links thimerosal to childhood neurological diseases.
However, it is still a very controversial area and 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, which prompted California to vote the state law banning thimerosal from vaccines given to children under three.
But the law can be waived when the paediatric vaccines is in short supply.
Each year, approximately 36,000 people in the US die from influenza and its complications and at least 200,000 are hospitalised.
Young children and the elderly are among those most vulnerable to serious, even fatal complications from influenza, and during the 2004 flu season, more than 150 children in the US died from influenza and many more were hospitalised as a result of complications.
No other vaccine-preventable disease kills more people in this country, according to the HHS.