Federated Farmers says the Government's decision to bring agriculture into its proposed emissions trading scheme (ETS) by 2015 is "highly disappointing".
And it now wants the Government to argue in Copenhagen next December - when details of the global new deal on post-Kyoto emissions are negotiated - for agriculture to not be included in carbon schemes.
"The Government must seek to remove agriculture at Copenhagen in December," said Federated Farmers president Don Nicolson, of Waimatua.
"While we support efficient and sustainable resource use, we have big concerns over the impact of an ETS."
The Government is relying on carbon-trading through its proposed ETS to help it meet a target of a 10 to 20 percent cut in carbon emissions on 1990 levels by 2020.
Nearly half of the nation's total emissions (48 percent) come from the agriculture sector - mainly methane emissions from 10 million cattle and 33 million sheep - while in other developed countries, the agricultural contribution averages about 12 percent.
In 2007, the total NZ greenhouse gas emissions were 75.6 megatonnes of carbon dioxide equivalents with agriculture contributing 91 percent of the methane and 96 percent of the nitrous oxide.
"This announcement means farmers will not only have to pay additional costs on their energy inputs like other businesses, but will also have to pay for their animals' emissions," said Mr Nicolson.
He claimed that farmers would have no choice other than to cull livestock to reduce their on-farm emissions.
"This is the equivalent of New Zealand experiencing a drought lasting several long years," he said. "Is that what New Zealand wants?"
Federated Farmers complained at the Labour Party conference at the weekend - on the eve of today's Government's announcement - even if agriculture was not "enrolled" in the ETS until 2018, it would be too short a run-up.
"A super tanker takes many kilometres to stop and nine years is insufficient lead-in time to radically change business or farm," Federated Farmers dairy chairman Lachlan McKenzie told the Labour Party conference in Christchurch.
He said that agriculture accounted for 16 percent of all private debt, worth $46 billion, which had been lent "on the basis of current agricultural practices".
"Millions of years of ruminant evolution cannot to be corrected in the next nine years," he said.
Instead of phasing in agriculture's contribution between 2018 and 2029, the Government should consider a "seismic shift" in policy for an "all-in" enrolment deferred until 2043 to give time for markets, and farmers and their debt-burden to reach an equilibrium. "If not, the entire economy is placed in jeopardy," he said.
But the Government said today that it not only expects to enrol on-farm emissions by January 1, 2015, but that under the previous framework, it had been expecting farmers to be brought on board by 2013, at the end of the first Kyoto commitment period.
Mr Nicolson said New Zealand was not a big emitter like China, the United States or Europe, and none of these had so far included agriculture in their emissions trading systems.
"While Prime Minister John Key kept his promise to bring our entry date in line with that of Australia's, the Federation is still adamant there is no place for agricultural emissions in the ETS," he said.