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The South Australia Government has rejected 11 council applications to maintain a genetically modified (GM) crop ban in their area.

The decision means Kangaroo Island will be the only part of South Australia where GM crops cannot be grown.

In April this year, South Australia lifted its 16-year moratorium on GM crops across the mainland, but local councils were given six months to apply to be designated a GM crop cultivation-free area.

It was the result of a compromise the Liberal Government made with Labor after the legislation reached a stalemate in State Parliament.

For the councils to remain GM-free they had to demonstrate the policy provided an economic benefit to the region.

It could not include matters of human health or environmental impacts, as those are managed under Commonwealth legislation.