Federation president Don Nicolson said he intended trying to unite organisations representing world food producers to push for an exemption when the Kyoto Protocol was reviewed, or reset, in 2012.
Even though agriculture contributes half New Zealand's greenhouse gases, at the very least, he wants ruminant animals exempted.
Mr Nicolson said in an interview taxing the productive sector was the wrong approach when the world was short of food.
The population would grow to nine billion by 2050 and taxing efficient and sustainable-food-producing New Zealand farmers would concentrate production in less sustainable regions of the world.
"We think that being world leaders in a country that relies so much on agriculture exports puts us in a unique position. We know it [the emissions trading scheme or ETS] is not going to pay dividends."
Instead, the focus should be on protecting food production, such as harvesting water for irrigation to secure food production in dry years.
He appeared to have doubts about the National Party's ETS policy, saying he was unsure about specific details.
The party campaigned on a commitment to implement "a well-designed, carefully balanced ETS" that included agriculture.
"We, however, will not support a scheme that compromises New Zealand agriculture's international competitiveness," the party's agriculture policy stated.
National's proposed changes to the ETS would meet six principles: strike a balance between environmental and economic interests; it would be fiscally neutral; would be closely aligned with Australia's planned ETS; would encourage the use of new technology to improve efficiency and reduce emissions; issue emission permits in a way that does not discriminate against small and medium enterprises; and would be flexible enough to respond to progress in international negotiations.
The party did not support the previous government's proposals, which put the burden on processors, as that did not offer incentives for farmers to change management.
Extra costs imposed on farmers would result in reduced stock numbers. How National would implement the ETS was not stated.
Act New Zealand, a likely coalition partner for National, appeared to more strongly reflect farmers' opposition, having campaigned for the "dumping of the dopey emissions trading scam".
Several reports have calculated that at an international carbon price of $25 a tonne, the cost of the ETS for a 4000-stock unit sheep and beef farm would be $4000 a year from 2013-18 and $40,000 from 2030.
For a 350-cow dairy farm, from 2030 the ETS would cost $41,000.
The incoming government has promised to replace the Fast Forward research and development fund with a dedicated $20 million a year centre to research greenhouse gas emissions from livestock, to increase by $25 million a year funding for the Foundation for Research Science and Technology and a similar boost for research into food and the primary sectors.
While the ETS was a serious threat to primary industry, Mr Nicolson said just as important were changes to the Resource Management Act, more targeted government spending to generate growth, not just redistributed wealth, and local government returning to its core business and functions.
He said farmers would welcome a stronger approach to protect their property rights and an end to what has been seen as an aggressive, antagonistic approach to pastoral lessees.
National has promised to take a new approach to tenure review and voluntary negotiations to secure access over private land.
"The tenure review process has become largely discredited, with the Labour Government's agenda leaving many runholders angry and disillusioned," the party's policy said.
The policy promised negotiations with lessees would be on a good-faith basis, pastoral lease rents would be tied to a property's earning capacity and at a level allowing lessees to maintain the property at an acceptable level.
It would also recognise that runholders could look after the land just as effectively as the Crown.
Some lessees face 5900% rent rises because of changes in the rent-setting methodology.
The party said public access over private land should only be achieved following voluntary negotiations.
"Farmers have been granting sensible public access to their properties for generations. To try to force unrestricted access public access across all land would have been highly invasive and confiscatory of private property rights," its policy said.