South Australia is lifting its ban on genetically-modified crops, but councils still have a choice.

The ban had been in place for 16 years, and the Government has made multiple attempts to lift it.

Independent reviews have estimated that the GM ban created a $33 million loss in canola crops alone since 2004.

Primary Industries Minister Tim Whetstone says the latest negotiations faith with the Opposition has led to a “workable” outcome.

“Today is a positive day for our farmers and regional communities, having that moratorium lifted,” Mr Whetstone said.

“This takes away any advantage other states have had and the economic constraints we've lived under for the past 16 years.

“This gives farmers the choice and will bring research and development programs our way.”

Local councils that wish to remain GM-free have been given six months to apply to an advisory committee that answers to Mr Whetstone.

The minister said the ban will be kept in place for Kangaroo Island because of the demands of its export markets.

One of the state’s major farming lobbies said welcomed the “extraordinary” news.

“Today we've finally seen a breakthrough in this debate that the industry has been working on since 2004,” Grain Producers SA chief executive Caroline Rhodes said.

“We've seen a compromised position that, whilst not ideal, does give an opportunity for some sensible legislation to go through parliament and give certainty to the industry.

“Seeding is already underway in South Australia and while farmers won't be able to get a crop in this year, I know there is huge appetite and interest in trialling GM canola varieties that are grown across mainland Australia and seeing how they perform in South Australia.

“I expect growers over the next few months will be engaging not only with local agronomists, but with their interstate counterparts about what this will mean for their farming environment.”