A senior health official confirmed five doses had remained at the end of the day and didn't tally up with records, so that the possibility some people hadn't received the correct vaccine dose couldn't be ruled out.
Any of the 732 border workers, frontline health workers and over 65s vaccinated that day could have received a placebo.
The Ministry of Health has not contacted any of those potentially affected.
Vaccinologist Helen Petousis-Harris, a member of the government's Covid-19 immunisation implementation advisory group, told RNZ a prompt investigation as to what occurred should be followed by those affected being contacted by health officials.
She said a mistake would have happened during the process of readying the vaccine for use.
"As we know, they come frozen and have to be thawed out, so once they're thawed in the little vial that they come in, the vaccinator will add saline or salty water. That will be inverted a few times and then the vaccine will be ready to go...
"If somebody takes a vial that's empty and puts in saline, the person will effectively receive a placebo. They won't receive any vaccine, so of course these sorts of errors need to be identified quickly and the person contacted."
She said it was important that those potentially affected were advised so that they could arrange another vaccination dose, if they believed they needed it.
"The concern is if somebody hasn't had a full dose is that they might not develop as much immunity to that does as somebody who's had a full dose. People getting a lower dose can still make an immune response.
"But I guess first of all you've got to determine what might have happened and go through the process of investigation and then contact people who may have been affected by that.
"There's absolutely no harm in terms of the vaccination or the vaccination process. It's just going to be important to make sure that people are aware so if required they can be revaccinated for example."
National director for the Covid-19 vaccination and immunisation programme Jo Gibbs said a full investigation into the incident was under way. She added the Ministry of Health had a "principle of open communication with any patients involved".
Gibbs said contact would be made once the circumstances of the incident were fully understood, so people could be given appropriate advice.