Biological Farmers of Australia says the Government's Carbon Pollution Reduction Scheme could cost farmers using environmentally friendly methods of production.
The BFA says better carbon soil sequestration by landowners who utilise biological systems without emissions-intensive farm chemicals should be accounted for.
The BFA submission to the Government green paper advises that agriculture be brought forward into an emissions trading scheme before 2015 for organic farmers who don't burn out carbon in soil.
"While we applaud policy moves towards reduced carbon pollution, discounting agriculture from a proposed ETS omits what could arguably be the biggest single optimal positive impact on carbon abatement and sequestering: soils," BFA director Dr Andrew Monk said.
"Organic and biological farmers should be given the opportunity to 'opt-in' to an emissions scheme from 2010.
"Organically managed soils are active models of an agricultural system which can deliver carbon sequestration and emission reduction benefits right now."
Soils under organic management have the potential to store carbon in organic matter or stable humus factions for up to 1000 years, the BFA says.
No synthetic chemical inputs in organic farming means CO2 emissions from organic farmers can be 40–60pc lower per hectare than non-organic.
"Organic farmers have to date internalised the costs of a production system that provides environmental benefits," Dr Monk said.
"It's now time for stronger policy and research and development recognition of the merits of organic production in Australia."