The state cited evidence from medical studies, which found that those who opted out from measles and pertussis vaccines were 22 times more likely to get the measles and six times as likely to get pertussis.
The flu kills about 86 children, from infants to teens, each year, according to the CDC.
The state is backed by the CDC, which insists that the flu vaccine is safe. Still, some parents believe that vaccines are overused and not sufficiently proven to be effective or safe.
Suspicions linger that compounds within vaccines are responsible for autism and other disorders when given to children early in life.
Children 6-months to 5-years-old enrolled in a daycare or preschool have until Dec. 31, 2008, to receive both the flu and pneumococcal vaccine. New Jersey requires the most childhood shots for day-care and school admission among all states in the nation.