New World St Martins, Pak'nSave Papanui and Pak'nSave Moorhouse are beginning a three-month trial of the technology from Wednesday.
Foodstuffs South Island said it was seeing some people repeatedly target its stores, even after being trespassed and hoped identifying repeated offenders early would prevent more harm.
"Everyone deserves to feel safe at work and when shopping," a spokesperson said on its website.
"When someone is violent, threatening or aggressive in one of our stores, our specialist, trained team reviews the incident. Only after careful assessment is an individual added to the FR watchlist."
The facial recognition system collected the image of everyone that enters any of the three supermarkets and cross-referenced the images of individuals on the watchlist.
If the system detected a person on the watchlist, the system would send an alert to trained staff at the store.
"Two trained team members manually review the alert, decide whether it is a match, and if so, what response is appropriate. This may include observing the person, contacting Police, or intervening to ask them to leave the FR Store - if it is safe to do so."
The company had engaged with the Office of the Privacy Commissioner and done privacy risk testing to ensure stores were compliant.
"We have worked, and will continue to work, closely with privacy experts to ensure compliance with New Zealand's privacy requirements."
