The West Coast Regional Council has given "partial support" to some of the proposals under the government's Pricing Agricultural Emissions document.
But it raises concerns about psycho-social, health and economic impacts on the region's largely rural community.
"We are extremely concerned at the impact this proposal will have on our communities," the submission for the council's Resource Management Committee said.
Incentive payments to reduce emissions should not come from reduced production, or promoting different land use, the council said in one of ten key points the submission raised.
"Council supports maintaining the integrity of the agricultural farming sector on the West Coast," it said.
The government had put "international reputation above the health and wellbeing" of the sector.
"Council would like to see investigation into the psycho-social, health and economic impacts of this proposal on rural communities, such as the West Coast prior to the adoption of any part of this proposal."
The proposed farm-level levy to reduce gross emissions needed to be modified to ensure it delivered sufficient reductions "in an equitable manner that is not detrimental" to the farming sector.
Instead, a system oversight body with key representation from the farming sector and affected parties is being recommended to ensure the system delivers.
The council is not convinced a free-range market-based system based on tradable methane quotas would achieve the desired outcomes any better than a split gas levy approach, which would be applicable to all farmers.
It cites heavy centralised administration costs and complex trading platforms due to the free-range market approach.
It also wants the price levy system, including for fertiliser, separated from the NZ Emissions Trading Scheme (ETS).
"Council prefers farm-level management."
Council agrees with introducing reporting obligations aligned to the business of an emitter rather than to a specific landowner - and investigation of collectives for monitoring, evaluation, verification and reporting.
It is calling for a two-tiered levy rate for pricing agricultural emissions, with separate pricing for long lived gas and methane - and for the system to be separated from the ETS.
Council supports revenue recycling that invests back in the agricultural sector, something supported by farmers and mana whenua, it said.
Farmers and growers being recognised for their on-farm carbon sequestration from riparian plantings and management of indigenous vegetation is supported by council as "a core component" of any agri-emissions pricing system.
It does not support instigating an interim processor-level in 2025 if the government does not have the farm-level pricing system ready by then - given the "setup and abandonment costs".
Local Democracy Reporting is Public Interest Journalism funded through NZ On Air.