A judge should have found a farmer of genetically modified canola was responsible for anticipating the impact of his crop and harvesting methods on his neighbour's organic farm, an appeals court has been told.

Prominent QC and former West Australian governor Malcolm McCusker is representing Kojonup organic farmer Steve Marsh who wants to overturn a Supreme Court ruling which struck down his compensation claim.

Mr Marsh had sought $85,000 in damages from his former childhood friend Michael Baxter and a permanent injunction that would stop Mr Baxter growing GM canola in the future.

The canola seeds blew onto his property in 2010 and he later lost organic certification for 70 per cent of his land.

However, in May last year WA Supreme Court Justice Kenneth Martin comprehensively rejected Mr Marsh's claims and awarded Mr Baxter more than $800,000 in costs.

Opening the appeal case today, Mr McCusker pointed to the swathing harvesting method used by Mr Baxter.

He said it created a real chance winds could blow the GM canola off two paddocks on his Seven Oaks property and onto Mr Marsh's Eagle Rest farm.

"His honour should have found a reasonable person in his position should have anticipated this could have happened," he said.

"It's the manner with which they harvested which caused the problem."

Mr McCusker said Mr Baxter's decision to use the swathing harvesting method was legitimate but the benefits were outweighed by the risk it posed to Mr Marsh's organic certification.

"You really have to look at the balance of interests of the two parties," he said.

"Although there were some reasons [for swathing], they weren't so important as to outweigh the duty to take reasonable care.

"There was a real risk the swathes sitting on top of stalks could blow onto the neighbouring property.

"He could have without any imposition of any kind, simply direct harvested elsewhere."

Mr McCusker told the three appeal judges the trial judge was "in error" to rule there could be no claim for damages without physical injury to person or property.

"There was no basis for his honour saying this is a wholly novel claim," he said.

Mr McCusker said Mr Baxter had a duty of reasonable care to ensure his GM canola did not contaminate his neighbour's organic farm and affect his certification.

"It was a risk which was foreseeable," he said.

Mr Baxter's lawyer Patricia Cahill said it was uncontested evidence that the GM crop did not contaminate Mr Marsh's organic wheat crop and the impact would have been the same if it had been a normal crop.

"There was no real difference to incursion of regular canola," she said.

Case 'not about GM versus organic'

The case has attracted international interest and provoked debate on the merits of GM crops.

Mr McCusker said this case was not about whether GM was harmful or organic food was better.

Anti-GM protesters in support of organic farmer Steve Marsh outside the hearing. ( ABC News: Nic Perpitch )

"The heart of this clash between two neighbours is a question of how two systems of agriculture can co-exist," he said.

"The answer is, they can if prudence and care is taken."

The appeal hearing is set down for three days.

About 30 anti-GM campaigners holding placards protested in support of Mr Marsh outside the court.

Louise Dunn said it came down to freedom of choice.

"I know the GM farmers say they should have freedom of choice to grow GM food," Ms Dunn said.

"But the freedom of choice principle is freedom of choice as long as you do no harm to others. And this has done harm to an organic farmer by losing him certification and his livelihood."