Fresh Choice Green Island owner John Moyle (52) said as a result of the cyclone he had to cancel the store’s planned fresh fruit and vegetable promotion week.
Transport coming out of Auckland had been seriously affected, as had fresh food out of "the food basket of New Zealand", Hawke’s Bay.
"New Zealand is a fragile country. We have one main trunk line, one state highway that runs the length of the country, a couple of ships and a very old infrastructure," Mr Moyle said.
Supermarkets in the lower South Island sourced much of their stock from warehouses in the North Island.
That reliance on the North Island had not left them with many alternatives, he said.
Stores and consumers would be hit hardest during winter, once orchards had been harvested.
While orchards had not yet been affected, he said it would be noticeable in the coming weeks and months.
Apples, pears, grapes, strawberries and kiwifruit would be most affected as well as cut flowers and wine.
He said the cyclone would have ongoing effects on transport, wages, power, diesel and fertiliser. This would cause prices to rise as businesses tried to meet higher costs.
He was unsure whether rural producers and orchards would recover before next season, Mr Moyle said.
"They’ll be unable to pick the ones that have survived. There will be a lot of waste. In a way, we’re all going to struggle."
In recent decades, fresh food production on the Taieri Plain and in Central Otago had declined, unable to compete with the scale and sunshine hours of the Bay of Plenty and Hawke’s Bay regions.
While the growing periods were about five months a year in Southland, they could reach up to 10 months in Northland.
A spokesman for Fresh Choice head office told him the cyclone’s impact meant the retailer’s fresh fruit and vegetable promotion would be postponed indefinitely, Mr Moyle said.