The West Australian Department of Agriculture and Food has called on the organics industry to allow for tolerance of genetically modified organisms (GMO) within its guidelines.

The department has made the first ever submission on GMO tolerance to the Organic Industry Standards and Certification Council, which represents the six companies licensed to give organic accreditation.

The submission followed the outcome of a WA Supreme Court case, in which organic farmer Steve Marsh's bid for compensation over a claim of GMO contamination was rejected.

Mr Marsh, an organic certified farmer in WA's Great Southern region, alleged his farm was contaminated by GM material from the property of his neighbour, Michael Baxter.

Mr Marsh claimed GM canola from Mr Baxter's property spread onto his farm and caused him to lose his organic certification on more than half his property.

But the presiding Justice Kenneth Martin rejected Mr Marsh's case in what was seen as a landmark ruling.

The Organic Industry Standards and Certification Council secretariat Marg Will confirmed to the ABC that DAFWA had made the first ever submission to the council on GMO tolerance.

Australian Organic chair Andrew Monk says the industry anticipates a spike in organic grain production and there should be a review of the application of organic and GMO guidelines to avoid future court battles.

Dr Monk says the standards for the end product should not be relaxed, but 'some lessons can be learnt' with regard to the application of organic and GMO planting guidelines.