NZ authorities have launched an emergency vaccination program to tackle an outbreak of a deadly strain of meningococcal that's killed six people this year.

Six deaths amid a spike in meningococcal infections have spurred New Zealand authorities to launch an urgent vaccination scheme for one region.

The country's Ministry of Health says the 29 cases of meningococcal W - a particularly deadly strain of the disease - nationwide this year are more than double 2017's figure.

Seven of those cases and three of six deaths nationwide have been in the northern-most Northland region, qualifying as a localised outbreak.

Health Minister David Clark on Monday announced agencies had acquired 20,000 doses of an in-short-supply vaccine and were launching an urgent public vaccination program targeting children under four and teens in a bid to stop the spread.

Authorities aim to have children vaccinated through schools before the Christmas holidays, but admit the time frame makes the task a challenge.

The strain, meningococcal serogroup W, has a particularly high mortality rate and has become increasingly common around the world in the past decade.

Those that have died across New Zealand have ranged from 11 months to 61 years old.

The same strain has been hitting parts of Australia, including 36 cases of the disease reported in Western Australian so far this year.