Agriculture Minister David Carter expects the sector to remain part of the emissions trading scheme that's now under review.
And he's told his Australian counterpart that the two countries need to work closely together on their climate change policies.
Mr Carter has been in Canberra for his first meeting with Australian Agriculture Minister Tony Burke.
And Mr Carter emphasised the need for Australia and New Zealand to co-ordinate their approach to emissions trading.
He says Australia is in the early stages of developing its emissions trading scheme and hasn't yet decided whether agriculture will be included.
Mr Carter says National campaigned on a review of the previous government's climate change legislation and that review has now started.
He says although it's impossible to preempt that review it's likely agriculture will be included in an emissions trading scheme, particularly given the profile of greenhouse gases emitted from New Zealand, with agriculture responsible for just under 50% of emissions.
Mr Carter says New Zealand cannot expect to make progress around meeting Kyoto liabilities unless agriculture is included.
He says it's important there are means available for farmers to reduce their emissions rather than simple reducing their livestock numbers.
Trans-Tasman trade disputes
Mr Carter says he and Mr Burke also discussed the ongoing trans-Tasman trade disputes over access for New Zealand apples, and some other horticultural products, into Australia and the current block on Australian honey into New Zealand.
He says they both acknowledged it was of paramount importance to maintain a free trading position between the two countries.
Mr Carter says both countries have their specific biosecurity concerns.
But Mr Carter says he emphasised to Mr Burke that all decisions have to be based on real science, not the emotion that has often surrounded some of the debates, particularly with regard to apples.