The Auckland Women's Health Council is shocked at figures showing that only 40% of infants are protected against group B meningococcal disease.
It says figures in a report completed by the centre in April suggest that the majority of six- to 17-month-old infants are protected against the disease.
The council says many parents thought the vaccine would last for life.
In fact, protection lasts a matter of months, not years, adding that only 50% of children receive an important fourth "booster" dose at 10 months of age.
Spokesperson Lynda Williams says many parents were not properly informed about the vaccine and many have been lured into a false sense of security about how well their children are protected.
The Ministry of Health says it cannot know for sure how many people are protected after the $200 million vaccination programme.
Ministry adviser Alison Roberts admits many parents who think their vaccinated child is protected could be wrong.