A food charity has been asked not to distribute food rescued from the floods until it can agree on checks with the Ministry for Primary Industries to ensure it is safe.
Kiwi Harvest rescued eight tonnes of packaged food, approximately 25,000 meals, from a flood affected supermarket in Auckland.
However, MPI asked it to stop distributing the food because it had been touched by floodwaters.
MPI deputy director general for New Zealand Food Safety Vincent Arbuckle said there were all sorts of risks in floodwater.
"We've got potential human sewage, dead animals, rotting foliage, potentially even chemicals, so flood waters are a complete worry," Arbuckle said.
"Everyone should assume if a food product comes in touch with flood water it runs a major food safety risk."
Kiwi Harvest chief executive Angela Calver said the standard had always been to dispose of food which had been touched by floodwaters.
"There's a lot of things that can be in floodwater, but having been in the food industry for a lot of years, and understanding food safety, I believe there is a protocol where we can clean it up. Obviously, you wouldn't do that with anything that wasn't packaged," Calver said.
Arbuckle said he had spoken with Calver and everyone involved was committed to getting the food to families safely.
"There has been food secured from supermarkets that has safely gone into food banks after careful checking. And that's all we are asking, that we work together with food rescue organisations to make sure that risk is minimised," Arbuckle said.
MPI was open to future discussions on a new safety standard for flood affected food, he said. This could include looking at what countries like Australia did in similar circumstances.