Australia's system of organic certification will come under intense scrutiny when two neighbouring farmers do battle in the Western Australian Supreme Court in a test case on genetically modified crop contamination.

Organic farmer Steve Marsh, from Kojonup in the state's Great Southern region, is suing his neighbour Michael Baxter for alleged negligence and nuisance.

Mr Marsh claims genetically modified (GM) canola seed blew onto his farm in 2010, causing him to lose his organic status.

He says he is prepared to risk his 480-hectare property to defend his right to farm without interference.

"It's totally about freedom of choice," Mr Marsh said.

"The GM proponents, they've argued for their rights to grow and use GM, this tool in the toolbox.

"All I'm asking is for the same right to be able to produce a GM-free product which we've traditionally done for years.

"I think that's very important because as farmers we should have the right to run our business and produce products that we choose to."

Mr Baxter has declined to comment, but says he will vigorously defend himself.

He is being supported by the Western Australia Pastoralists and Graziers Association (PGA), which says the organics industry has set an impossible zero tolerance standard for genetic modification contamination.

PGA's grains committee chairman John Snooke says Australia has adopted an international contamination threshold of up to 0.9 per cent, which allows for things like pollen flow and other accidental events.

"The zero threshold is causing this, it is a threshold that is unachievable in agriculture because we operate in nature," Mr Snooke said.

"It's not what Australian agriculture is about.

"We have a live and let live philosophy, we have a common sense approach, we operate in nature. Now, all that has gone out the window sadly, because the organic certifier employs a zero tolerance for unintended presence of GM canola."

Mr Marsh is being supported by litigation lawyers who are acting for him pro bono.

The Safe Foods Foundation, a not-for-profit operation set up to campaign against genetic modification, is also trying to raise up to $500,000 to pay for the additional court costs.

The foundation's director Scott Kinnear says the organics industry sees the case as a fight for its survival.

"In Australia we have a chance to produce clean organic foods, and we have been producing clean organic foods, and it's do or die for us now," Mr Kinnear said.

"With the advent of GM canola we have to take a stand now, we have to take a stand strongly, which is what we are doing with Steve Marsh and with using [lawyers] Slater and Gordon.

"We will take this case with all of the vigour and energy and effort the organic industry can muster to defend the right to produce organic food GM-free."

In Europe, Canada and the United States organic certifiers allow for some genetic modification contamination, but Mr Kinnear says this was imposed on the industry in those countries.

"Organic foods in Australia were here well before the advent of GM technology, it's not a natural technology, it's something that wouldn't occur in nature, just as chemicals are not natural," he said.

"We accept a threshold of contamination with chemicals and organic because chemical farming was here first.

"[But] organic farming has come along, it's been articulated, standards have been developed, we do not accept later technologies that come along and impinge on our production systems."

Farmers across the WA wheat belt planted a record amount of GM canola this year and the State Government is spending $9 million on a program to encourage the world's best GM research projects at facilities in Merredin and Katanning.

Food and Agriculture Minister Terry Redman says the industry has clear guidelines for managing the contamination issue and a record amount of canola was sold into Europe's strictly non-GM market last year without any contamination concerns.

"We do have systems in place that can effectively separate different grains from each other, we've been doing that for many, many years," Mr Redman said.

"When you look at GM grains compared to other grains they're just another grain in the system.

"If we use barley as an example, there's about 25 different breeds of barley, they all look the same in a bucket, but we've been effective at keeping those separate grain markets."

Lawyers for the farmers will be in court next month for a directions hearing.

The case should be heard before the end of the year, but regardless of the outcome, the opposition is likely to make GM contamination an issue when the state goes to the polls in next March.

Labor's agriculture spokesman Paul Papalia says consumers are being denied a right to choose non-GM because of inadequate labelling laws.

He says the Government refuses to say if GM canola grown in WA has been fed to livestock.

Under current labelling laws, this would not have to be identified.

"Seriously, this is a consumer issue, the consumers of WA shouldn't be told by the Barnett government, by the Premier [Colin Barnett] or by the Minister for Agriculture that they should feed their children food that contains GM products," Mr Papalia said.

"If they want to do that for their own children or own grandchildren, that's their decision, but they need to provide the information to consumers so they can make their own choice."

Mr Redman says Labor is attempting to play on unfounded fears about the safety of GM products.

"Clearly they're looking at this to raise a level of public profile which in my view is scandalous and I think they're putting a whole level of uncertainty out there about safety issues that are frankly wrong," Mr Redman said.

Sean Murphy will have more on this story on Landline at 12:00pm on Sunday on ABC1.