The food safety body is looking into pest management at all Woolworth's supermarkets after rats were spotted in two South Island stores.
A video online showed a mouse scurrying across a salad in the deli section at the Eastgate Countdown last Wednesday.
Woolworths stores director Jason Stockill said staff disposed of the salad contaminated by the mouse, but did not close the deli.
He accepted the supermarket should have done more.
"It's unacceptable what we did as a store team, as a leadership team as well," he said.
"Our learning is we should have disposed of more than just the two bowls ... and we'll review all our processes and procedures to make sure they're right, and if that means we've got to do more training we'll absolutely do that."
Meanwhile, the South Dunedin Countdown, where 19 rats - including two in the past 24 hours - have been trapped since Friday, will remain closed until 48 hours after zero rats have been sighted.
"We've decided to make sure that we can get the confidence back with our customers and our community and the store team, that we won't actually open the store until we have zero captures and then we'll wait 48 hours after that before we open the store," Stockill said.
Woolworths 'taking the appropriate steps' - union
The union representing supermarket workers was pleased Woolworths' general processes around pest management would be looked at.
First Union national organiser for food Ross Lampert said employees were concerned.
"Our members take this seriously, they want to work in a clean, healthy and safe environment. We feel that the company is taking the appropriate steps at this point to get the situation under control," he said.
Woolworths needed to increase its awareness around pest management, Lampert said.
"I would be surprised if there were not issues in other supermarkets as well," he said.
"I know that the way that supermarkets operate; they have places where birds or other pests can come into the store easily ,because either their front doors open on to the road or back doors are often open, because they have trucks coming and going all the time, so it's particularly difficult to prevent.
"It's obviously something concerning to all New Zealanders."
