Staff cleared out the freezers and dumped meat and seafood.
The discarded food will go to the Rotorua landfill. Countdown has insurance to cover the loss.
By opening yesterday morning, all the meat and seafood freezers were empty and being cleaned out ready for fresh stock once the fault was repaired.
Removed stock had to be dumped, according to food safety requirements, Mr Green said.
"We'd much rather throw it in the bin than put customers in jeopardy. We have very strong safety measures.''
When he arrived the temperature in the freezers was about 15C.
Mr Green said the store's food safety policy was that food in chillers needed to be kept at 4C and -18C for frozen food.
Bacteria could get into the food and make people very sick, so they weren't prepared to take the risk with the temperature well above requirements for about two hours before the fault was picked up, he said.
"It had obviously been off for a while. Anything that has been out of the fridge for too long is no good.''
Customers would not have to wait long for fresh stock to arrive, Mr Green said. Daily orders were arriving as normal to replenish repaired freezers.
Mr Green said he hoped the freezers and chillers would be back on and filled by the end of today.
"We have staff at the doors greeting people and letting them know we are still open and people can buy meat from across the road.
"Online shopping is still available,'' he said.
Karen Short had popped in to Countdown to pick up meat for a family dinner when The Daily Post was there.
She said it was an unavoidable inconvenience.
"I'll just get everything else I need here and pop across the road for the meat,'' she said.
Brad Lindsay was looking for sausages but settled on tinned fish for his lunch. He wasn't put out by the lack of fresh meat, he said.
"It's just one of those things. It's not like Marmite _ gone forever it seems. I'm sure there will be meat tomorrow or we can go elsewhere'' he said.
Grace Ward said she was planning a vegetarian meal because she couldn't be bothered shopping elsewhere.
"I'm sure we won't die not eating meat. It will be vegetarian or take aways for us,'' she said.