Mr Mackley, who farms 800ha near Horsham in Victoria, has changed his crop rotation and his marketing, no longer able to claim he is GE Free, a label he wore with pride.
During a visit to Dunedin last week, he told the Otago Daily Times that GE was "firmly rooted" in Australia but resistance to GE crops was growing among farming communities, as pressure from companies and lobby groups associated with the GE industry increased.
Farmers using GE were producing bulk crop commodities that had no demonstrable advantage over those produced by farmers using traditional methods, he said.
Mr Mackley, who is in New Zealand with his wife Robyn, is on a nationwide speaking tour with Green MP Steffan Browning.
Mr Mackley is a long-time opponent of GE.
His troubles started when his neighbour was about to harvest his GE canola crop.
Two days of heavy rain meant some of the windrowed canola ended up on his farm, in a paddock earmarked for GE-free canola.
Some of the GE canola started to sprout and took hold in his paddock.
To avoid contaminating his crop, Mr Mackley changed his rotation policy and instead of following a legume crop with an oil seed crop, like canola, he had to plant a grain crop.
That grain crop was not up to his usual standards but he had no choice if he wanted to avoid contamination, he said.
"I'm doing what I can to limit the effects.
"There are better ways to farm.
"You can fix the paddock but you cannot fix the industry.
"The money put into GE research would be better spent put into research on soil."
Some farming methods were damaging the soils and Mr Mackley advocated more environmentally friendly farming practices.
A separate side effect was the extra travelling he now had to do around his farm because of the changed rotation.
Instead of driving 14km to a paddock and doing one large job, he finds himself travelling to the paddock several times to do smaller jobs.
He already had concerns about contamination because there was nowhere he could buy canola seed in his area where the retailers would give a legally enforceable guarantee the seed was GE-free.
Also, he had to change his marketing from being GE-free.
"If you advertise as GE-free, buyers construe that as having none - not 1% or 0.9%.
"GE is seen a cheap low-grade product, end of story.
"The message that I am GE-free made me stand out."
The pricing differential was starting to show, as was the change in percentages of GE-free canola compared with the GE crops, Mr Mackley said.
Tonnages of GE crops supplied to collection points had fallen.
GE-free crops were getting about $A50 ($NZ65) a tonne more.
Asked how fellow farmers had reacted to his opposition to GE, Mr Mackley said it was a forbidden subject among some of his friends who did grow GE crops.
Others would offer their private support and were pleased someone was providing opposition.
Mr Browning visited Mr Mackley's farm recently and came away concerned that GE contamination could easily happen in New Zealand.
Asked whether the GE debate had died away in this country, the MP said the public perception might be that GE had gone away.
However, Crown Research Institutes, industry bodies and corporates were still active behind the scenes, promoting genetic engineering.
New Zealanders were seen as having too much resistance to GE crops but industry pressure to adopt the technology was continuing to increase, Mr Browning said.