A West Australian organic farmer who sought to sue his neighbour for $85,000 after claiming genetically modified canola had contaminated his farm, could now have to pay more than $800,000 in court costs.

In June, the Supreme Court rejected Kojonup farmer Steve Marsh's compensation case against his former childhood friend Michael Baxter.

Mr Marsh had alleged GM canola swathes blew onto his property from Mr Baxter's farm in 2010 and caused him to lose organic certification over 70 per cent of his land.

The organic farmer announced his decision to appeal the court's ruling in July.

Justice Kenneth Martin has now ruled to allow limits on costs to be removed, given what he said was the "unusual difficulty, complexity and not to mention an undeniable importance of the matter".

In orders handed down on Friday, Justice Martin said the draft estimate of taxed costs and disbursements claimed by Mr Baxter against Mr Marsh was $803,989.

That included almost $339,000 in fees to Mr Baxter's legal team to prepare the case.

The awarding of costs is subject to any application for a stay of orders pending the outcome of the appeal.

Justice Martin also said attempts by Mr Marsh's legal team to show Mr Baxter did not ultimately bear the primary responsibility for costs in the case, were "wholly misplaced".

"To allow the plaintiffs' application for disclosure by Mr Baxter in respect of any agreements from the PGA [Pastoralists and Graziers Association], Monsanto or Mr Baxter's crop insurer would, on my assessment, very much amount to the sanctioning of an impermissible fishing expedition," Justice Martin said.