A child fully immunised against Meningoccocal B has died of the disease in the Waikato.
It is the first confirmed fatality from the epidemic 'B' strain of the disease of someone who had received a full course of the vaccine.
The Government launched its $220million vaccination campaign against the strain in 2004.
The Waikato District Health board confirmed the child - aged under-five - died earlier this month.
It said the death was a "sobering reminder to remain vigilant for the disease and seek treatment as soon as possible".
Waikato Medical Officer of Health Dr Anita Bell said the child's parents did all they could, and sought help as soon as possible.
But she added: "While the immunisation programme is effective protection for most, there will be a few who remain vulnerable.
"The reasons for this are unclear, and impossible to predict from person to person."
Dr Bell said New Zealanders needed to stay alert for early warning signs and seek medical assistance as soon as possible for all strains of meningococcal disease.
National Meningococcal B Immunisation Programme Director, Dr Jane O'Hallahan, said the tragedy was a reminder of why a vaccine programme had been launched.
"Our focus must remain on breaking the natural cycle of this disease epidemic through the immunisation programme, and saving lives where we can."
News of the death follows the release of Ministry of Health figures that showed meningitis killed five children in July, the highest monthly death toll in nine years.
The data showed that for the six months to May 2006, there had been proportionately as many cases of the epidemic strain of the meningococcal disease in fully vaccinated children (1.1 per 100,000) as there had been in partially vaccinated and unvaccinated children (1.2 per 100,000).
However, Dr O'Hallahan said preliminary results from an independent study showed the vaccine worked.
" Those who are not fully immunised have a five times greater risk of getting the disease," she said.
"While it is not a guarantee for everyone, the vaccine remains our most effective weapon in the war against meningococcal B."
Dr O'Hallahan said the younger a child was, the more vulnerable they were to the disease.
"It is important that children and young people complete all three doses," she said.
The Ministry of Health says it is critical that young babies who began their vaccinations before they were six months old, have all four doses.
Under-20s have until the end of the year to complete all three doses, while newborns and under-fives will continue to be offered the programme until 2009.
In its early stages meningococcal disease can look like the flu. A baby or child might have a fever, be crying or unsettled, refuse drinks or feeds, vomit, be sleepy, floppy or hard to wake, dislike bright lights or have a rash or spots.
An adult may have a fever or headache, a stiff neck, joint pain and aching muscles, vomit, be sleepy, confused, delirious or unconscious, dislike bright lights, have a rash or spots.
Shots in the dark?
The meningococcal epidemic campaign finished in July.
* More than 1.15 million children have been immunised against the epidemic strain of the disease since the vaccination campaign started in July 2004.
* More than 3 million injections have been given, with the Ministry of Health saying 80 per cent of under-20s have completed all three doses with 80 per cent effectiveness.
* There were 35 cases of meningococcal disease last month, the highest monthly total since before children were fully vaccinated with three doses.
* Since 1991, there have been more than 5900 cases and 239 deaths from meningococcal disease. Less than half were confirmed as the epidemic strain.