Australia has pledged to fight its corner in a trans-Tasman battle with New Zealand over apple imports.

Peter McGauran, Australia's Minister for Agriculture, Fisheries and Forestry, said the country will defend its quarantine processes after New Zealand launched a complaint against its neighbour at the WTO.

New Zealand has complained of delays in finalising a quarantine and inspection programme for its apple exports to Australia, McGauran said.

The Australians claim that New Zealand's orchards contain the bacterial disease fire blight, which is not present in Australia.

"The Australian government will strongly defend its actions and policy determination on the basis of science," McGauran said. "I am confident that our approach to quarantine is consistent with the WTO rules."

McGauran said the first step in the WTO dispute process was a consultation stage, which required Australia and New Zealand to try to settle their differences out of court.

"It is always Australia's strong preference to settle WTO disputes bilaterally," he said. "We will continue to work with New Zealand towards this end, but any resolution must be within the context of our science-based quarantine regime and very low-risk setting."