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Federated Farmers is concerned the amount of land required for planting - between 1.3million and 2.8million ha - would have to come from sheep and beef farming properties.
The Forest Owners Association also believes that new land will be found on farms and cautioned farmers would need the best advice to avoid repeating past mistakes.
While the previous National-led government had a climate change target of zero emissions by 2100, Labour's target is the more ambitious 2050.
Federated Farmers' climate change spokesman Andrew Hoggard said while the 620 page, 173 findings and 78 recommendations report was a ''door stopper'', it still deserved ''careful scrutiny''.
''We're pleased to see the commission recognises the credible elements for long-lived [carbon dioxide and nitrous oxide gases] and short lived gases [methane] to be treated differently,'' he said in a statement yesterday.
He noted the commission's chapter on land use change suggested land devoted to arable and horticulture would expand two or three-fold by 2050.
''Much more worrying to the provinces is the recommendation that the amount of land planted in forests will need to increase by between 1.3 and 2.8million hectares,'' he said.
''Most of this land is currently used for sheep and beef farming.''
He estimated the 2.8million ha in forestry represented about 20% of all of the current 14million ha of land under agriculture.
''That sort of land use change would be devastating for many rural communities in terms of job opportunities and sustaining the social and economic fabric of small towns,'' Mr Hoggard said.
Forest Owners Association president Peter Weir said the scope of new planting, proposed to make New Zealand carbon neutral by 2050, would have to plant 100,000ha a year, which had only been done in 1994, for each year of the next three decades.
''It's vital that the Government works closely with all landowning groups to ensure an efficient and equitable transition to an envisaged decarbonised economy,'' he said in a statement.
Farm Foresters Association president Neil Cullen said in the same release he believed the only sufficient land area to achieve the planting goal would be found on farm land.
''Farmers will need to have access to the best advice on how to go about planting woodlots, and so avoid the mistakes too prevalent in the past, such as poor planning for road access at harvest time,'' he said.
It was not just a government job, but farm organisations had to have a central role in helping the transformation of farm properties into an integrated land use operation, with a substantial investment in forestry, Mr Cullen said.
Business New Zealand's chief executive Kirk Hope welcomed the report, noting the commission pointed out that the sooner New Zealand began the transition to a low-emissions economy, the less costly the transition will be.
''Key to doing this will be to maintain the international competitiveness of New Zealand businesses and ensuring that the burden faced by New Zealand consumers and families is not disproportionate to other countries,'' Mr Kirk said in a statement.