Epidemic strain meningococcal disease cases were already showing a decline before the vaccine was introduced, official figures show.
The sharpest drop, however, occurred after 2004 when vaccination started.
Ministry of Health records of epidemic strain cases between 1997 and August 7 - last Monday - show the peak of the disease at 2001, when 296 cases were recorded among those under 20.
Numbers began falling the next year, with 218 cases, and 189 cases in the year after that.
The mass immunisation programme for under 20s started in July 2004, with 145 cases recorded for the whole year. A sharp drop occurred the next year, with 82 cases. More than halfway through this year, only 28 cases have been recorded.
The $222 million immunisation programme has been labelled a waste of money by critics who said the disease was already waning without the vaccine - a notion disputed by health officials.
Two children have died from the epidemic strain of meningococcal disease this year. The death of a Waikato toddler is the first fatality of someone fully immunised against the epidemic B strain. The other child who died was too young to be fully vaccinated. Another death in the under-20 age group cannot be confirmed as being caused by the epidemic strain.
Risk analyst Ron Law, a critic of the vaccination programme, said the programme had been a failure.
"For an individual who gets meningococcal disease, it's irrelevant what strain it is. Society was told this vaccine was going to wipe the epidemic. It hasn't. The $222 million could have been put into preventing 500 diabetes deaths or the 1500 highly preventable deaths in the health system."
An independent study by Victoria University which took into account background factors affecting the disease rate, such as seasonal change, age and ethnicity, found that children who were not immunised were five times more likely to contract the epidemic strain than those vaccinated.
The ministry says no vaccine gives 100 per cent protection, and estimates that the programme has saved about three lives.
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, or until disease rates indicate the programme can be ended sooner.
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