A West Australian farmer who sued his neighbour and former friend after genetically modified canola blew onto his land, contaminating his organic crop, faces an $800,000-plus court costs bill that could devastate him financially.

In his 2014 lawsuit against childhood friend Michael Baxter, Steve Marsh argued he had lost organic certification for 70 per cent of his farm at Kojonup, southeast of Perth, because of contamination from the herbicide-resistant canola crop next door.

Mr Marsh had sought $85,000 in damages, but lost the trial and was instead ordered to pay Mr Baxter's court costs of more than $800,000.

Mr Marsh challenged those decisions last year, arguing Mr Baxter's harvesting method known as swathing - which allowed loose Roundup-ready canola to lie on the ground and then blow onto the neighbouring farm - was irresponsible.

However, the High Court denied him leave to appeal last month and a stay on the costs order was lifted on Tuesday.

The anti-GM Safe Food Foundation raised about $1 million to help pay Mr Marsh's legal costs, but not enough to cover Mr Baxter's and the costs of the appeals.

"He will get a very, very large legal bill," Safe Food Foundation spokesman Scott Kinnear told AAP.

"He's in a very difficult position."

Whether the Safe Food Foundation would do any further fundraising to help Mr Marsh would be up to him, Mr Kinnear said.

Multinational agribusiness Monsanto had agreed to cover Mr Baxter's legal costs.