Stocks of influenza vaccine are being shifted from some centres that have supplies to others that are without, in a bid to get the most at-risk people vaccinated.
There are roughly 800,000 flu vaccines in the country, but due to the ordering process, some centres have ended up with more than others.
Medical centres are sending out notices to their patients telling them they are all out of flu shots and people will have to wait until the end of April to get it.
Wellington's Island Bay Medical Centre told its patients in an email:
"Influenza vaccination sticks have been exhausted throughout the country. This means that our planned vaccination clinics for influenza have to be cancelled until further notice. While this is disappointing there are some positives to note. Because of the social isolation underway, the scope for spread of influenza is greatly reduced. We should get stock in before the end of level 4. This delays the immunization date, which means the effectiveness will be extended well into October. We often see influenza spikes in September/October so this delay is not a bad thing."
Kelburn Northland Medical Centre told its patients:
"Booking for Flu vaccinations are currently on hold due to low stock nationwide.
Unfortunately, we are unable to take any bookings for flu vaccinations, as the supplier has advised us not to expect further vaccine supplies until mid to late April. We will update our website when flu vaccines are back in stock and patients eligible for a funded vaccine will be able to book in. Once we are permitted to provide flu vaccines to our non-eligible patients we will advise of this. This situation is outside of our control and we thank you for understanding."
The Ministry of Health said this was an issue of distribution, not a shortage.
Royal New Zealand College of General Practitioners medical director Bryan Betty said the vaccine usually arrived at a warehouse in Auckland before being distributed.
"There seems to be some sort of maldistribution that's occurred, where certain centres or pharmacies seem to have a lot of vaccine and other areas are really low."
Dr Betty said it was a first-in, first-served system, which in the past had worked well.
"The problem we've run into this year is potentially the demand for the vaccination. A lot of centres are running out quickly and suddenly there's no more vaccination up at the central distribution point."
Local public health offices were now trying to locate stock and shift it to where it was needed most, he said.
Priority groups such as the elderly, people with existing health problems, and those in lower socio-economic environments are being targeted first.
Dr Betty said he was not entirely confident that the people who needed it the most would get it in time.
But he said the ministry was now limiting medical centres and pharmacies to 60 vaccines per order, and was looking to change policy that currently prevents pharmacies from giving centres their stock.
Pharmac said more shipments of vaccines were coming, with the first due early next week.
In total, it will deliver 1.7 million vaccines to New Zealand. That includes the roughly 800,000 already here - a 30 percent increase on the previous year.
The remaining vaccines will be delivered in batches through until May.
The Ministry of Health said it was working with Pharmac and the supplier to better manage the stock, because there had been much larger orders than usual.
It also said it was worth noting that flu immunisation did not normally start until April, and the flu season usually started in late May.