The comments have drawn criticism from Australian vegetable industry group Ausveg, whose public affairs manager William Churchill said the debate had been fuelled by trans-Tasman rivalry.
"There is a fierce competitiveness between Australia and New Zealand when it comes to who can produce the best. You only need to look at the time-old argument about who invented the pavlova.
"The head of Tomatoes NZ is probably saying 'I would rather eat a New Zealand tomato over an Australian tomato,' regardless of had it been irradiated."
Mr Churchill said irradiation was a safe method which avoided the need to fumigate with methyl bromide - a process that took a week to complete and damaged the ozone layer.
He said the tomatoes were given "a quick zap" of radiation which killed the fruit flies, but did no damage to the food itself.
Mr Churchill said "scaremongering" comments from the Greens about the safety of irradiation were disingenuous and irresponsible.
Greens' biosecurity spokesman Steffan Browning said irradiated food should not be imported into New Zealand.
Irradiation destroyed vitamins and other nutrients in fruit and vegetables, he said.
Mr Browning said there were many alternative methods such as heat or cold treatments, controlled atmospheres and ozone treatments.
"Problems with strong pesticides used by importers are not fixed by replacing them with irradiation.
Mr MacLeod of Tomatoes NZ has called for compulsory labelling of all irradiated fresh produce, saying consumers had the right to know.
"Unlike Australia, New Zealand does not have compulsory labelling of fresh produce - so under the current regime, unless retailers take it upon themselves to clearly label irradiated Australian tomatoes and capsicums, consumers won't know."
Horticulture NZ chief executive Peter Silcock supported calls for tough labelling requirements.
"Kiwis don't get enough information about the origin of the food they buy and eat," he said.
"We must at the very least have point-of-sale labelling for irradiated tomatoes and information provided to food service, hospitality and catering providers."
Ms Kaye said the Australia New Zealand Food Standards Code mandated that irradiated foods were clearly labelled.
"This includes at point of sale and as an ingredient in food. Consumers can ask restaurants and cafes if ingredients in the food have been irradiated."