Potatoes are hard to come by meaning there will be less choice of chips for consumers, says Potatoes New Zealand boss Chris Claridge.
But both big supermarket chains are talking down the prospect of a chip shortage.
North Island potato processors are experiencing difficulties due to extended periods of wet weather, affecting crop in Pukekohe, Matamata and Horowhenua.
Claridge says supply won't be back to normal until the beginning of next year.
"We're getting reports that up to a third of crop has been lost in the Pukekohe region. Overall with the crop of the country, we think we may be about 20 per cent to a quarter down, and so we're seeing correspondingly high levels of prices in the marketplace," he said.
A Foodstuffs spokeswoman said its chip supplier to New World and Pak 'n Save supermarkets was not affected, despite a statement and some stores on Sunday posting notices warning customers of "trouble stocking potato chips".
Claridge, however, said the supply issue was affecting crisp manufacturers as they had a smaller percentage of the total crop in New Zealand.
"The serious issue here is that Kiwis take food security as a given, and I think it's a luxury that we can't guarantee. Land availability and climate change are impacting this staple commodity."
A Countdown spokesman said the supermarket chain was not experiencing any shortages of potato chips in its stores.
"Our suppliers have said that there could be fewer potato chips supplied in the coming months, however we will work directly with our suppliers to manage this."
The shortage had no impact on fresh or frozen potatoes, or other snacking categories, the spokesman said.
Claridge said the North Island was predominantly experiencing supply issues.
"South Island manufactures are not finding supply issues as difficult, but again its weather dependent," he said. "North Island brands are going to experience difficulties, South Island brands not as much."
Claridge would not reveal which specific brands were experiencing difficulties.
"Planting is increasing well in the South Island, in the North Island it is difficult because it still keeps raining so getting adequate land prepared and putting in to do planting is difficult seasonally all year round but its not made easy by the fact that land availability is an issue."
The potatoes shortage means there will be fewer crisps for consumers, he said.
"There will be less choice and brands will experience difficulties."
He said he didn't expect the price of crisps to rise in coming weeks and months.