A farmer in Western Australia's Great Southern region is suing a neighbour after his property was allegedly contaminated by genetically modified canola.

Stephen Marsh's lawyers lodged a writ with the Supreme Court today.

It is alleged his neighbour Michael Baxter was negligent in allowing GM canola to blow onto his farm.

Mr Marsh, who farms wheat on 478 hectares at Kojonup, says as a result of the GM contamination about 70 per cent of his farm was stripped of organic certification in December 2010.

He says this means he was unable to sell his crop for a premium.

His lawyer Mark Walter says his client is seeking damages for economic loss as well as an injunction to prevent future contamination of the farm.

"They've spent 10 years building up their organic status," he said.

"It's now going to take them anywhere between five to 10 years to get that status back.

"In terms of dollar figures and how that translates, it's still early days."

The Safe Food Foundation's director Scott Kinnear says it is an important test case.

"It's the first time Australian laws about competing land uses involving GM and non-GM crops [will be] tested," he said.

"Certified organic premium varies from 50 to 100 per cent above what the conventional price of wheat would be.

"So, they can be very significant premiums of hundreds of dollars a tonne and that premium [Steve] used to enjoy would have been a sizeable sum of money which he's lost."

The foundation has pledged to financially support Mr Marsh in his court battle and says his lawyers are acting pro-bono.

It is urging the state's farmers not to plant GM crops until the case has been resolved.

Lawyers believe the matter could go to trial early next year.