The Ministry of Health says it doesn't recognise vaccines a person has received overseas.
Vaccinations that are administered overseas can not be added to a person's vaccination record, or verified for their authenticity.
RNZ understands there could be more than 1000 people in contact with the ministry to have their overseas inoculations recognised here.
Director-General of Health Dr Ashley Bloomfield said a system for verifying overseas vaccinations is being worked on urgently, ahead of a planned rollout of vaccine certificates next month.
Early this year, a woman and her partner received their first dose of the Pfizer vaccine in Northland, when there was a Covid-19 scare prior to Waitangi Day.
Weeks later they received a second dose of the vaccine while in the United States.
Eight months on, the vaccine has not been added to their vaccination record here in New Zealand.
"Even though it's recorded on the little white card that we were given in New Zealand, it has the type of vaccine being Pfizer, it has the date it was administered, the batch number, and whatever other information is on there, it's all recorded on the same card," the woman, who asked to remain anonymous, said.
"But as far as New Zealand's Ministry of Health concerned, we have only had one vaccine."
She said officials are sympathetic to their situation, but have no answers at the moment.
"As silly as it seems, it seems like it's an administration issue.
"It seems like they don't have the ability to record it, although I find it hard to believe. They say they are unable to record any vaccines that were given outside of New Zealand."
The Ministry of Health has provided few options for how to rectify the situation.
"It was suggested that if we wanted two doses recorded we could have another vaccine.
"They're still chasing us to get dose number two, even though we've had it and we've told them on numerous occasions. They have said that we can get another dose."
She said she is concerned about how the vaccination issue will affect her chances of getting a vaccine certificate, which Deputy Prime Minister Grant Robertson said will be available from next month.
And while she is open to getting a third shot of the Pfizer vaccine - with some countries now giving out a third booster shot - she said it would still have implications down the track.
"On the face of it, in a few months I could have another vaccine and I will have had three, which equals the initial two and the booster.
"But what I'm concerned about is if I travel overseas, my record is not going to be correct because my New Zealand records all simply shows that I've had two, when in actual fact I've had three."
The Ministry of Health officials she has dealt with say it is a big issue, with possibly thousands of people in a similar situation - having been vaccinated with doses that are not recognised in New Zealand.
Bloomfield said it is a multi-faceted issue.
He said the ministry is currently coming up with advice around which vaccines - AstraZeneca, Janssen or Moderna for example - it will recognise for future travel into the country.
But it is also working on how to verify and register people's overseas vaccinations.
"At the moment, if people have had one or both vaccinations abroad, it's not easy to enter those into the Covid immunisation register," Bloomfield said.
"They might have had their first one here, the second one, same vaccine, Pfizer, in the States or something.
"We're working out now a process where we can verify that and then enter that into the Covid immunisation register so they can be classified as fully vaccinated."
Bloomfield said he hopes there will be a system in place by the time vaccine certificates are rolled out next month.
Prime Minister Jacinda Ardern said there will not be any adverse implications for people if the ministry is not ready with a verification system by the time certificates are being introduced.
"I'm sure we can find a workaround," Ardern said.
"We have no intention of invalidating someone's legitimate vaccine if they've received it abroad so it's just a matter of making sure we've got a fix for it."
Bloomfield admits that verification of vaccines will be easier in some countries than others, but there will be no discrimination against people who got a vaccine in less developed nations.