A teenager contracted meningococcal B though he was fully vaccinated against it.
The Health Ministry said it was reviewing the case of the Auckland boy who contracted a mild case of the epidemic strain of meningococcal disease but has now made a full recovery.
Around 700,000 doses of the vaccinehave been given to children and teenagers under the immunisation programme.
Meningococcal B Immunisation Programme Director Dr Jane O'Hallahan said it was impossible to get the disease from the vaccine, which does not contain live or complete bacteria.
"The youth appears to have had a less severe case of the disease. It is possible that the vaccine provided partial protection for this person and lessened the severity of the disease," Dr O'Hallahan said.
The boy became sick about a fortnight ago and spent two days at Auckland's Middlemore Hospital before getting better.
Dr O'Hallahan said for all vaccines there were a few people who do not develop full immunity.
"A small number of vaccine breakthroughs are expected as the number of people being fully vaccinated increase. But the fact remains that vaccination is the best protection against this fearsome disease," Dr O'Hallahan said.
To be fully immunised a person needs to have three doses of the vaccine and then it can take up to 28 days after the third dose for immunity to fully develop.
An estimated 7000 children and young people are being vaccinated every day.
In the latest available figures, up to May 1, more than 95 per cent of children aged from one to four years have had their first dose of the vaccine in the Counties Manukau District Health Board and Eastern corridor of Auckland DHB.
About 90 per cent of these children had had their second dose and 79 per cent had completed the three doses. In the school-age group of five to 17-year-olds more than 94 per cent had had their first dose and 86 per cent had completed their third dose.
Dr O'Hallahan said the programme was very successful.
"These are children and young people who have historically had lower immunisation rates."
In total 172,000 children and young people were fully vaccinated.
