About 25,000 women take the four contraceptive pills affected: Brevinor, Brevinor 1/28, Norimin and Necon.
The pharmaceutical company Pfizer does not expect them to be back in stock until mid-February next year.
"It's a mixture of problems," Pharmac's acting medical director Dr Ken Clark told Checkpoint.
"Even well before COVID times, the company responsible here has signalled that they were having some supply issues and production issues. On top of that, as we're all aware COVID-19 has added a whole different dimension in terms of slowing up supply chains and production of all sorts of medicines, including unfortunately oral contraceptives."
He said he does not know why supply was an issue before the COVID-19 pandemic.
"The company did signal low that they were having difficulties with keeping up with demand and supply. Even back then we went and looked for some alternatives to help so that … women were not left without the exact formulation that they had been using."
Some of the stocks of particular contraceptives will run out in the next few weeks Dr Clark said.
"The reality is that some of them, [new supplies may not come] until February next year. Naturally, we will hope for better than that. But to some extent, these are matters out of our hands.
"There are several thousand women using these particular contraceptives. Of course, many women use oral contraceptives, but these particular ones are not the most common.
"But there are still thousands of women that use these products. What in practice it means is that there are other oral contraceptives available that work and work as well, but may not unfortunately suit these women as well, particularly in terms of the effects on their menstrual cycle, et cetera.
"So, of course it's not ideal where we would much rather this was not happening. But we are asking that women and of course health practitioners, talk and think through options in terms of other oral contraceptives or for that matter other forms of contraception."
Doctors and medical centres have been warned of the coming shortage, but that warning has been short, he said.
"It was very short in terms of us finding out about it as well. But as soon as we've known about it, we've communicated. But there's no doubt that in some cases this notice will be short. And we apologise for that.
"I can truly say it's not of our making, but that doesn't make it easy for women, and of course their prescribers."
Pharmac is looking at whether the drug supplied Pfizer is in breach of contract because of the shortage, but Dr Clark said the companies Pharmac deals with are "tremendous" in terms of maintaining backup supplies.
Although the supplier is working hard to help, it cannot guarantee security of supply, Dr Clark said, but he believes they are acting in good faith.
"There are a number of medicines where we've had signalled potential shortages… There always a small number of medicines, where that's the case. But in 2020, given the circumstances, that number is of course greater.
"There are tens of medicines where there are issues about supplies. I'm pleased to say though that in all of those, because of stock that's held, because of efforts from companies and of course from Pharmac, that those supply issues have been mitigated."
Paracetamol is not in critical short supply, he said.
"It's a general mix of all sorts of things, including hypertensive medicines and others. With the issues with supply, it's affecting all sorts of aspects of medicines, not just of course critical care medicine, it's anything."
In a statement to Checkpoint, Pfizer New Zealand said: "Due to a manufacturing delay there is a current shortage of some Pfizer oral contraceptives, including NORIMIN™ and BREVINOR.
"Pfizer New Zealand is focused on providing a consistent supply of these contraceptives for patients, and are committed to actively resolving this matter.
"Normal supplies are expected to resume February next year."
Pfizer said patients who need to replenish their supply should discuss alternative contraception options with their healthcare professional.