"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."