There are "hundreds and thousands" of flu vaccine doses in the South Island and people taking out their frustration on healthcare workers is "not OK", the Prime Minister says.

Jacinda Ardern was responding to questions at a press conference today about mounting tension in the South amid an apparent shortage of the flu vaccine.

"Their region has vaccines, I checked about four days ago," she said.

This comes after the Otago Daily Times reported chaos at Dunedin medical centres administering the vaccine yesterday.

Aurora Health Centre doctor Jill McIlrath said the South Dunedin practice was only able to order about 60 vaccines each week.

"We have about 1500 patients who are in the vulnerable category who we have been working to get vaccinated."

The clinic had administered 587 vaccinations so far, and was having to tell people to wait until more arrived.

Ministry of Health director of health Dr Ashley Bloomfield said today the ministry would "absolutely respond to the issue" at the medical centres in Dunedin.

He said a shipment of flu vaccine was meant to have come to the South Island at the weekend but the ferry was cancelled.

That meant it was a few days late, he said.

"There are still hundreds of thousands of doses out there in the system that can be delivered," Dr Bloomfield said.

Ms Ardern said one of the challenges had been that the vaccine had to be distributed to multiple district health boards and multiple medical centres and pharmacies.

Responding to a question about Dunedin medical centre staff copping abuse from people desperate for the flu vaccine Ms Ardern said it was "not OK".

"Don't take out your frustration on frontline healthcare workers."