"Avsec takes security matters very seriously and that this is a relatively rare occurrence given the nearly 5 million passengers screened per year at the AKL International terminal," A Civil Aviation Authority spokesman said.
Once the investigation was complete if any changes need to be made to procedures then they would be tested and then implemented.
There would be no further comment by the CAA while the investigation is ongoing.
During the incident images of long queues emerged on social media and Auckland Airport said it would restart screening, but said it would take some time to clear the backlog.
Several members of the public tweeted about the security shut-down, with one saying that "Kiwi travellers are very relaxed in the face of massive delays".
At least four flights were affected.
Air New Zealand and Virgin Australia flights to Christchurch and Gisborne were delayed, as well as flights to the Bay of Islands with the same two carriers.