Pharmacists say they are stretched and tired, providing Covid-19 vaccines and passes on top of their usual workload.
More than 400 pharmacies were brought in last week to distribute vaccine certificates when the Ministry of Health's help centre was overwhelmed by up to 70,000 calls a day.
Pharmaceutical Society president Professor Rhiannon Braund said members got just a few days' warning but they were willing to help.
"When these decisions get made obviously it's quite quick. So there are lots of conversations about what is possible, and then suddenly, something happens. And so for a lot of the profession, they sort of felt that it was short notice.
"But I guess this is the nature of the beast right now, we just try to be as proactive and respond as quickly as we can," she said.
People were coming with problems other services haven't solved.
"In the first couple of days, these were quite time consuming, getting the pharmacists to get the system up and running, just navigating the portal. And of course, there were some tech issues because so many people were trying to get the vaccine passes, coming up to the cut-off date."
She expected pharmacies would only get busier with holiday-makers away from home this summer, and new Covid-19 response measures.
"The rapid testing that's coming online in the next week or so, the announcement about the childhood vaccinations ... I think we're actually going to see quite a surge [in work]."
She said it had been "a really busy year" and the workforce was "stretched".
"People are tired and I just hope that people can take some time to look after themselves, as well as the patients."
People getting vaccines or vaccine passes from pharmacies do not have to pay a fee.
The Ministry of Health had issued 3.25 million vaccine certificates by yesterday afternoon.
In a statement, the Ministry said it "reached out to pharmacies on Tuesday last week regarding the process for producing the vaccine passes, and provided training courses and other support on the Wednesday and Thursday to help them prepare for the system going live on Friday.
"We are continuing to provide ongoing support to pharmacies regarding My Vaccine Pass, and acknowledge and appreciate their efforts."