The applications of all 11 councils that applied to become a GM crop-free area were rejected, on the grounds they had not provided "sufficient evidence" on the trade and marketing benefits of being GM-free.
"Under the legislation councils had a once-off six-month opportunity to apply to remain GM free but under the Act passed by Parliament, applications could only be considered on trade and marketing grounds," Mr Basham said.
"The GM Crop Advisory Committee assessed the 11 applications and deemed there wasn't sufficient evidence to recommend designation as an area where no GM food crops can be grown."
Several councils expressed their disappointment in the process, with the City of Onkaparinga investigating means to reverse the decision.
The decision was praised by several industry bodies, but had anti-GM groups up in arms, with Greens MLC and fierce GM-free advocate Mark Parnell labelling the process a "cruel hoax".
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