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.
