Doctors say major problems getting access to flu vaccines is putting patient safety at risk and forcing them to cancel hundreds of appointments.
The Health Ministry insists the country has "plenty", but Newshub has learned one of the main suppliers to New Zealand has run out of stock.
Two days ago, the message from the Health Ministry was we have 800,000 flu vaccines and health teams were told to start vaccinating the most vulnerable.
"We're pretty busy," registered nurse Lucy Hassett told Newshub. "People are coming in for their flu vaccines. We're probably doing 80 to 100 vaccines per day."
But there's a problem. Newshub has spoken to GPs around the country who say they're either running out or have none left.
"The issue with the supply of flu vaccines in New Zealand at the moment is really frustrating and infuriating and actually, in my opinion, quite dangerous," Lumsden GP Dr Matthew Stokes said.
He told Newshub he's had to cancel hundreds of flu jab appointments.
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"This is across hundreds of patients," Dr Stokes said. "It's just not sustainable, especially considering the pressures we're under with COVID."
NZ Medical Association GP Council chair Dr Jan White agrees it's disappointing.
"It's incredibly frustrating to be out in practice not being able to deliver what you know is the right thing for your patients."
One doctor at a large practice in Christchurch told Newshub, "We have had to put on ten more phone lines to cope with demand.
"The flu vaccine issue is a crisis that is caused by Ministry mishandling."
Another doctor wrote, "We have over 250 patients which we have had to cancel as the vaccines have not arrived".
And yet another said, "It is ridiculous. It is infuriating to hear the Ministry tell our patients to 'make sure they get the vaccine cause there is plenty of supply' when it is NOT TRUE!"
But on Wednesday the Ministry reiterated it has "substantial" stocks.
"This is about making sure we get that flu vaccine to where it's needed, so it's a process of stock distribution," Director of Public Health Dr Caroline McElnay told reporters.
But It's clear that distribution isn't working. Healthcare Logistics, where most of the country's flu vaccine is dispatched from, refused to comment.
In an email obtained by Newshub and sent to doctors, the company states that "there are disruptions to the supply chain for the flu vaccine Afluria Quad, that they are out of stock, and backorders have been cancelled".
The email goes on to say that they can still supply another brand of the flu vaccine but only at 60 doses per order.
Newshub understands one group that does have a lot of vaccines is the pharmacies.
"My plea would be can we get something organised where vaccines can come back from pharmacies and into general practices where they're needed," Dr White said.
Rachel Newfield, the chief executive of Green Cross Health - a group that represents pharmacies, told Newshub, "We support the ability to safely share available vaccines but regulatory restraints don't allow this.
"We have raised this with the Ministry of Health."
Dr White said it has to happen with urgency.
"We can't have fridges full of flu vaccines that are not being utilised."
And that's exactly what we have - and the message from the Health Ministry is "be patient - we're working through the backlog".
Pharmac, the drug buying agency which organises the supply of flu vaccines for New Zealand, said around 1 million doses had arrived here.
Its director of operations Lisa Williams told Newshub: "Pharmac is in contact with suppliers regarding delivery dates" and additional shipments are expected between now and mid-May.