The association, which launched a consultation on changing its standards for growing organic crops under glass and polytunnels last month, asked whether the standards should outlaw fossil fuels.
Policy director Peter Melchett said: "Apart from air freight, heated glasshouses are the only thing with an organic certificate where 80 to 90 per cent of the carbon footprint comes from one single source. Everything else you do in organic growing is largely irrelevant.
"We have to cut 80 per cent of greenhouse gas emissions. How can growers conform to that by anything other changing how they heat their glasshouses?"
Dr Jill Vaughan, director of Delfland Nurseries and chair of the Soil Association's horticulture standards committee, spent £170,000 on a woodchip system. "The payback was something between two to three years but compared with other investments it was worth doing," she said.
Riverford Organic Vegetables operations director Rob Haward said heating under glass was expensive - £1m investment per hectare of glass and £400,000 in overheads. But it pushed up yields two-and-a-half to three times, he added.
"High input costs demand high yields of high-value produce to deliver a return on the initial investment and overheads," said Hawford. "Heat and carbon dioxide are the pull factors enabling good yields. Should standards change the heating system or fit around the system?"
Melchett said the association must keep at the "front of the curve". For now supermarkets were driving long seasons, but they may start carbon footprinting glasshouses and asking whether importing was a better option.
"To be in a position to say we have a 10-year programme to end with high renewable energy levels is attractive, but I'm not sure what it would mean for the grower," he added.
Soil Association members believe growing crops in bags or containers runs counter to the organic ethos. Senior producer adviser Astrid Toner said "growers principles are very clear: organic production should be in the soil".
- Deadline for responses to the Protected Cropping Green Paper is 9 July, visit: www.soilassociation.org/consultation.aspx.