Covid-19 Response Minister Chris Hipkins says up to 100,000 people are being given exemptions as they wait for their vaccine passes.
Speaking to Q+A's Jack Tame, Hipkins said more than half of those were people who had been vaccinated overseas, and many others had "name-related issues".
On Thursday, the day before the country moved into the traffic light system which requires vaccine passes in certain settings, about 70,000 people were being issued temporary exemptions for the My Vaccine Pass.
Hipkins told Q+A as of this morning that number had grown.
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"As of this morning, there were somewhere between 90 to 100,000 issues in the queue to be dealt with."
Asked if this many exemptions issued undermined the system, Hipkins said it would be sorted out quickly.
The issues could be easily resolved, but required talking to "an actual person", he said.
The wait time on the phone was about five minutes currently.
He said about 3.6 million passes have been issued in only a couple of weeks and the system had "gone remarkably smoothly".
There had been a lot of work around data and creating systems which normally would "take a lot longer", he said.
"Overall I am satisfied with the way it has gone. I'm sure with more time there will be things we could have done better."