The flights departed "from Auckland departed 45 minutes-1 hour late as Aviation Security required customers to go through security screening again," she said..
The re-screening of passengers had earlier started at about 8am.
Auckland man Carl Jackson was on a plane about to depart for Wellington when passengers were asked to get off and head back to security.
The delay meant he would miss a work meeting in the capital - although he said he would just dial-in instead.
He said no one panicked but there had been massive queues waiting to go back through security.
The airport spokeswoman said the first focus had been clearing all the departure lounges and planes, then finding the passenger responsible.
The terminal has CCTV throughout, she said.
"This will take some time and on top of that they haven't started re-screening yet. We just ask that people be patient with Aviation Security as they do their job. It's a security breach, this is just what they do."
The Civil Aviation Authority would decide whether the passenger would be prosecuted.
"It's a huge inconvenience for people who have already been screened and are now delayed," the spokeswoman added.
One frequent traveller said he had never seen anything like it.
"Just hundreds and hundreds queuing. Queue to get through security to Auckland is back to the regional departures. Maybe thousands impacted."