Booth said the proposals had created a lot of confusion and he believed many farmers, particularly beef and sheep, would be harshly affected by the proposals.
"The biggest thing coming out of this is the uncertainty it has created across the primary sector because what's been recommended is certainly not what we put forward to the Government," Booth said.
"The initial document, for example, included a formula that calculated each farm emission, which included incentives to try and reduce the carbon sequestered on your farm.
"What's come back does not include that initial formula, and while they're saying it's still available through another channel, it's going to be a much more complicated process."
According to Booth, farmers were limited in what they could do to reduce carbon emissions.
He said they could improve farm practices and efficiencies, but there wasn't yet the scope to reduce emissions by 25-30 per cent "overnight".
Booth said the main concern for a lot of people right now, however, was that the changes could mark the death knell for small, rural communities where farming was the lifeblood of the local economy.
"It's a fine line trying to strike a balance between the direction of travel we need to take and doing it in a way that's not going to adversely affect rural communities and populations," he said.
"We are world-leading farmers, so this needs to be more a matter of trying to promote emission-efficient farming, not destroying New Zealand agriculture.
"As the largest contributor to the New Zealand GDP, if agriculture hurts, then our economy hurts too."
DairyNZ was involved in the He Waka Eke Noa consultation and backed Booth's concerns about the recommendations' potential impact on rural communities.
Chairman, Jim van der Poel, said the Government's emissions-pricing proposal threatened the viability of farming businesses and was not acceptable.
"DairyNZ is committed to securing a fair pricing system for farmers and we would like to see the Government revert to the He Waka Eke Noa recommendations put forward in May," said van der Poel.
"He Waka Eke Noa was designed as a whole farm system approach to reduce emissions, meet targets and give fair recognition and reward for planting farmers have done on their farms.
"We believe the Government's significant and unnecessary changes have undermined farmer confidence in the process and needlessly put the finely balanced cross-sector consensus at risk.
"We must reduce our emissions, but we can't drive blindly towards targets at all costs. We have to remember why we are doing this in the first place.
"The Paris Agreement is about reducing global emissions, not just New Zealand's emissions."
On the He Waka Eke Noa website, programme director Kelly Forster said the agricultural sector was concerned about the impact of the Government's proposals for agricultural emissions pricing, among other things.
She said the group was already having conversations with the Government about how to improve the proposals released by the Prime Minister.
"The Government's proposals were a double-edged sword – progress from where we started three years ago, but some concerning changes from the approach that He Waka Eke Noa recommended in June," she said.
"We started this journey when the Government passed a law requiring emissions reductions and legislating for agricultural emissions pricing by 2025.
"While nobody wants to see a new levy on farmers, it's a fact that emissions pricing is coming and we have to work to make it as manageable as possible."
Foster said those still arguing against efforts to reduce emissions were "ignoring reality" and that consumer expectations, locally and internationally, had shifted.
She said many competitors for New Zealand's food and fibre products were setting net zero targets and working to lower emissions from food production, so New Zealand could not afford to stand still.
Another area where the Government's proposals needed more work, Foster believed, was recognising sequestration.
Foster said He Waka Eke Noa had proposed a carefully balanced system that took on-farm sequestration into account when calculating each farm's levy bill.
She said the group proposed farmers would be able to "bank" the sequestration from a wide range of vegetation, including riparian planting alongside streams, woodlots and windbreaks as well as native forest.
"The Government's proposing recognising a more limited range of vegetation, only a fraction of what is actually being sequestered on-farm," Foster said.
"And it's proposing rewarding farmers in the short term through contracts and in the long term through including this vegetation in the NZETS.
"We need to take time to understand the practical impact of these changes and work with the Government to ensure genuine sequestration is appropriately recognised."
Foster encouraged farmers to get involved by putting forward their views on what would help them transition to the lower-emissions food production that customers and the community were looking for.
People have until tomorrow (November 18) to provide feedback on the Government's proposal.
The Northland Age contacted the Ministry for Primary Industries, which said it was not able to comment.
Minister for Agriculture, Damien O'Connor was also approached for comment, but did not respond in time for edition.
