Access is being restricted amid a surge of flu cases and high numbers of vaccine doses distributed. Pharmac has sent out more than 1.26 million doses so far - almost as many as for all of last winter.
Vaccines will be available only to people eligible for publicly-funded vaccination including the elderly, those with chronic illnesses and pregnant women.
Pharmac director of operations Lisa Williams told Morning Report suppliers had to predicted how much vaccine will be needed well before the start of the flu season.
"There's only a limited amount that can be manufactured each year - there's only a few companies that make it - and you do need to make the vaccine for the specific strains of flu that are circulating.
The World Health Organisation issued the decision about which strains of flu should be included in vaccines for the northern and southern hemispheres.
Global manufacturers were now starting to make stock for the northern hemisphere strains, and there were no more supplies of the southern hemisphere vaccine.
Ms Williams said Pharmac wanted to make sure the vaccine stock held by doctors and pharmacies was being used for people most at risk.
"There's not much stock left in the national store, but we would much rather have the vaccines out in the community than sitting in a national stockpile.
"We don't know how much is sitting in ... GPs' and pharmacies' fridges, and we haven't heard any reports of anyone turning up to get vaccinated and not being able to.
"We're just asking the people who give vaccines 'make sure you're managing the stock that's in your fridges and using it for people who're at most risk."
There is a plentiful supply of the version of the vaccine designed for young children, she said.
ESR (Institute of Environmental Science and Research) figures show influenza like illness is higher than usual for this time of year.
In Australia there have been more than 55,000 notifications of influenza this year, and at least 119 people have died.
Deaths from flu 'under-measured'
In New Zealand three people have died this season; rugby league player Zae Wallace, 20, and two people in Auckland - a 62-year-old and a 12-year-old.
"At the severe end it's a very sudden, quite extreme, illness," Professor Michael Baker said.
Prof Baker, from the University of Otago's Department of Public Health, has carried out research showing deaths from flu are under-measured.
"The research ... suggests we have an average of about 500 people die every winter in New Zealand from the flu but only one in 20 of them are recorded as flu deaths."
A minority of deaths are directly from flu, such as a rapid and overwhelming overwhelming viral pneumonia.
But flu kills in ways that often aren't recognised, he said, making people vulnerable to a secondary bacterial pnueumonia or to heart attack.
If you have the flu you should stay home and avoid contact with workmates, Prof Baker said.
Symptoms are fever, fatigue and aches, particulary muscle aches and headache, as well as the respiratory symptoms such as a cough or runny nose.
"You just have to go to bed for a few days", he said.
A vaccine offers some protection after a few days and full protection takes about two weeks.
"Typically it's around 50-60 percent effective at stopping you getting the flu and stopping bad outcomes."
The type of flu viruses circulating change rapidy so most hears the vaccine isn't usually a perfect match for the current strains, which is one reason it is not 100 percent effective.
"Even now there would still be benefit in getting vaccinated because we haven't seen the peak of the flu yet in New Zealand."
ESR said A(H3N2) and B/Victoria viruses are circulating in New Zealand and the 2019 seasonal influenza vaccine is good match for the viruses around at present.
