The country is running low on the Covid anti-viral drug Paxlovid, which helps keep sick patients out of hospital.
In a joint statement, Pharmac and Te Whatu Ora say there is limited stock in some areas because of the spike in Covid cases and higher demand for the drug.
Director of prevention, national public health service Becky Jenkins and Pharmac's director of pharmaceuticals Geraldine MacGibbon said some pharmacies had temporarily run out, and those with supplies were being asked to send them to places where there were shortages.
"We acknowledge the pressure supply issues place on the health sector, so are grateful to those who have helped redistribute stock of Paxlovid to help ensure that eligible people are still able to access it," they said in the statement.
The agencies were working with the distributor to get more.
Almost 20,000 courses of the drug arrived on Thursday and were being fast tracked for distribution.
Pharmac said it was trying to secure more Paxlovid to arrive in March and April next year.
Hospitals also have a good supply of the remdesivir infusion for Covid-19 positive patients, which is an alternative available for those who need further treatment.
On Wednesday RNZ reported that health officials were encouraging people to book a Covid-19 booster shot before Christmas if they believed they were at risk.
The past few weeks have seen a Covid hospitalisations creeping back up towards levels seen at the start of the year.
Now summer social gatherings could further increase infections and put vulnerable populations at risk, Te Whatu Ora Director of Public Health Dr Nicholas Jones said.
Public immunity waning as virus evolves
Otago University public health professor Michael Baker told Midday Report the shortage was bad timing with the country currently experiencing a fifth wave of the virus.
"Paxlovid is a very effective antiviral. You have to take it within five days at the start of your illness and it does interfere with the virus progressing with infection.
"Trials show that it is good at reducing symptoms of illness and keeping people out of hospital and also reducing the mortality risk.
"Particularly for older people and those [with] underlying illness, it can be a lifesaver."
He said it would be prudent to focus the available supplies on the elderly with underlying illnesses.
"This fifth wave is a bit of a surprise because it's bigger than the last wave, the fourth wave back in April.
"I think most of us were hoping these waves would get less intense over time and that doesn't seem to be the case. So this has big implications for how our need to continue managing this virus, which I think you could still say is effectively a pandemic in terms of how it's behaving.
"The big problems are waning immunity over time and also the fact that this virus is continuing to evolve and sometimes quite swiftly, and these new lineages that come through are succeeding because they're better at infecting us, and it's also had some big evolutionary jumps that again weren't expected."
"We all want it to go away and it's not doing that ... so we need to plan accordingly" - Otago University public health professor Michael Baker
There was a need for a consistent strategy to manage the threat "based on the fact that this virus is going to continue to cause these big waves that will sweep through the country".
"I don't think it's that predictable how it is going to behave from now on because we are seeing a very evolved new variant that is becoming very infectious internationally, and that may actually drive a longer way this time than anyone's expected."