They will not have to pay for the vaccine, but to be eligible they will have to be a Northland resident.
Pharmac has sourced 20,000 doses of vaccine that cover four types of meningococcal disease - A, C, W and Y. The cost is commercially sensitive, but it costs $700,000 to roll out the vaccination programme.
Director-General of Health Ashley Bloomfield said people had died from MenW as young as 11 months and as old as 61 years, but teenagers were the highest carriers of the disease, and under 5s were at the highest risk.
"The best way to protect all age groups is stop the carriage of the bacterium," Bloomfield said.
"If we get advice that we need to roll it out further, we will be looking closely at that advice."
He said people could not be compelled to be immunised but he hoped that 80 per cent of people in the target groups would be vaccinated, which would stop it being carried.
Northland was advised on November 6 about the possibility of an outbreak, and a technical advisory group reported two days later that there was in fact an outbreak.
But in May, Northland DHB clinical microbiologist David Hammer circulated a letter to DHB staff warning of a "significant rise" in MenW cases.
In his memo, Hammer suspected there would be a "whole lot more" cases over the winter as the disease spread "rapidly though areas where younger people congregate, such as schools, hostels, army barracks and university campuses".
National's health spokesman Michael Woodhouse welcomed the vaccination programme, but said lives had been put at risk because the response had taken too long.
"The Government needs to reassure New Zealanders that public will be made aware of any future outbreaks sooner and that they will be handled more appropriately."
Bloomfield defended the time it took to respond, saying the outbreak was only confirmed on November 8, and it then took time to secure the doses - as both Australia and the US were dealing with outbreaks - and develop the programme.
Pharmac was keeping a close eye on further sources of the vaccine in case more are needed, he added.
MenW was carried in the throat and spread by close contact, and Bloomfield said people in Northland were exposed to conditions to made them more susceptible to MenW, such as poverty, overcrowding, and close-quarter living.
There have been 10 deaths since January due to meningococcal disease, six of them from MenW.
They have included Whangarei seven-year-old Alexis Albert, whose grieving mother pleaded for a nationwide vaccination and awareness programme, and Kerikeri 16-year-old Dion Hodder, who died in Auckland City Hospital soon after becoming ill during a Motutapu Island youth camp.
Northland DHB chief executive Nick Chamberlain said it would be challenging to vaccinate 20,000 people before Christmas.
"We are hopeful that more vaccine will become available so we can vaccinate the entire population under 20 years, as we did in 2011 with the meningococcal C vaccination programme.
The location of the clinics will be confirmed as soon as possible, he said.
Meningococcal disease is a bacterial infection that causes meningitis - an infection of the membranes that covers the brain - and septicaemia, or blood poisoning.
While meningococcal B (MenB) has long been the dominant strain in New Zealand, causing two thirds of cases of the disease, there were growing concerns over the rise of MenW.
Medical experts say MenW can present differently to other strains, including severe respiratory tract infection such as pneumonia and, more so in adults, gastrointestinal symptoms.
Meningococcal bacteria are difficult to catch as they don't live for long outside of the body but are passed from one person to another through secretions from the nose or throat.
Within three to seven days after being exposed to the bacteria, meningococcal disease is typically first felt by the onset of a sudden high fever and is easily mistaken for other common flus and illnesses.
