The system sent an error message after deciding Richard Lee's eyes were closed, when they are clearly open.
It was not racism he suggested. "It was a robot. No hard feelings."
The DJ and aerospace engineering student had submitted the photo to an online photo checker at New Zealand's Department of Internal Affairs.
"No hard feelings on my part, I've always had very small eyes and facial recognition technology is relatively new and unsophisticated," the 22-year-old told Reuters.
Mr Lee is studying in Melbourne, Australia.