About 9000 women take Brevinor 1/28 and about 16000 women take Norimin/Necon/Brevinor, Pharmac said.
The issue lay with the manufacturer and was an issue pre-Covid but had been exacerbated by the pandemic, Pharmac acting medical director Dr Ken Clark said.
There were ongoing global constraints on all ethinyloestradiol and norethisterone products, he said.
"We recognise and acknowledge this situation will be disruptive for some people. If you take these oral contraceptives, we encourage you to talk with your prescriber about alternatives."
There might be more Necon that could be made available to cover the prolonged stock shortage of Norimin and Pharmac would provide more information about that as soon as possible, Clark said.
Family Planning national medical adviser Dr Beth Messenger said the shortage would leave many people without their first choice of contraceptive.
"The contraceptive pill is still the most commonly used contraceptive tool in New Zealand. Women need a reliable supply to protect against pregnancy and to support them with a range of medical conditions," Messenger said.
"At Family Planning we write more than 32,000 contraceptive pill prescriptions each year - we know how many people are potentially impacted by this shortage.
"We want to ensure these clients have good information about how they're to manage this shortage and we want to provide our clinical colleagues with information about the options they can offer their clients to manage through this shortage. We've already been contacted by GPs looking for advice and support about other contraceptive options that can be offered."
If you currently had a supply of any of the pills, you should continue taking them as normal until you ran out, she said.
If you already had a prescription the pharmacy was unable to fill or you needed a repeat, you would need to talk to your prescriber about other options.
You might be able to use another pill type while the supply is disrupted or consider a different contraception type such as the injection or an IUD.