Forest research institute Scion was given clearance last year to use cutting-edge gene-splitting technologies known as ZFN-1 and TALEs to alter the genetic code of pine trees to produce desired traits such as denser wood, faster growth and resistance to disease and drought.
An EPA-appointed committee found that although organisms resulting from the novel techniques would fit New Zealand's definition of GM, the techniques were close enough to a traditional plant-breeding method to be exempted from GM regulations. In clearing the new technologies, the three-member committee overruled EPA staff advice.
The Sustainability Council - arguing the approval placed the GM-free reputation of our food exports at risk - appealed, and the High Court last week found in its favour.
Among those leading the clamour for change is the science group leader at AgResearch, Dr Tony Conner, who says the ruling highlights that New Zealand's GM regulatory system is broken.
"Changes need to be made urgently, otherwise further innovation in New Zealand's genetic research will be severely stifled."
Scion says the regulations are seriously deficient and the ruling puts New Zealand at odds with other regulators.
But a third Crown research agency which is using the gene-splitting techniques in containment, Plant and Food, is more cautious - saying its food industry partners remain sensitive to negative consumer attitudes to GM products.
Council executive director Simon Terry, and others opposed to the uncontained release of GM organisms, argue that the judgment does not restrict the use of the two new technologies in confined research and identifies the need for only minor tinkering to clarify wording in the regulations.
The Environment Ministry plans to review the rules to "ensure they appropriately consider evolving technologies". Any recommended changes would need to be considered by Parliament. It says it is too soon to say whether the review's scope will be informed by public consultation.
In her ruling, Justice Jillian Mallon said decisions about what techniques were GM were for the Government to make and the EPA committee's judgment call "does not sit well with the purpose of the act or [its] precautionary approach".
The technologies in question were relatively new and intended to cause more specific and rapid changes than traditional techniques.
"There is no evidence before me which says that the environmental effects of these changes ... are established and therefore certain."
The techniques are among a raft of new technologies which aim to produce targeted mutations without introducing foreign DNA into the genome of the cell. But only the United States currently allows some of the techniques and claims that New Zealand risks falling behind are misleading, Mr Terry says.
Scion general manager of manufacturing and bioproducts Elspeth MacRae says the agency wanted to use the techniques to target changes that could be achieved with traditional breeding methods but would take many years and with less precision.
EPA chief executive Rob Forlong says the agency is studying the implications of the judgment, which acknowledges that a pivotal clause in the regulations was "not well drafted".
The committee which cleared a path for forest research agency Scion to use GM techniques outside the lab was headed by a scientist who had worked with the agency on previous GM pine research.
A second appointee to the three-member committee was a lawyer who went on to act for Scion in a court case.
The panel chosen by the Environmental Protection Authority to consider Scion's GM application was chaired by Dr Louise Malone, a bioprotection specialist with Plant and Food Research, a Crown Research Institute. Dr Malone has led, or contributed to, a number of research projects evaluating the impacts of GM techniques, including working with Scion scientists on transgenic pine experiments which found no impacts on insects and invertebrates.
Green MP Steffan Browning believes Dr Malone had a clear conflict of interest in chairing the decision-making committee which cleared the way for Scion to use novel GM techniques to develop new traits in pine trees.
But the EPA says Dr Malone's extensive experience in environmental risk assessment of plant biotechnology made her appointment appropriate. Chief executive Rob Forlong says her research interests had been declared and "it was evident that there was no conflict of interest". She had participated in studies which found both positive and negative effects in relation to GM organisms and she had never worked with the technologies under consideration.
Lawyer Helen Atkins, another committee member, had previously provided legal advice to Scion and went on to act for the agency in a court challenge to the Bay of Plenty Regional Council's regional policy statement, which took a precautionary approach to GM organisms. Mr Forlong said Helen Atkins did not act for Scion at any time during consideration of the application.
But Mr Browning said the EPA's predecessor, the Environmental Risk Management Authority, had problems with conflicts of interest and the agency needs to review its selection processes.
"I acknowledge the difficulty in getting genuine independence in a small country but we could have a better mix on the panels." He said increasing collaboration between scientists meant the current pool of Crown Research Institute personnel should not be a source for GE decisions.
The Auditor-General's Office recommends a precautionary approach on conflicts of interest and notes the "reasonable perception of an outside observer" is important when managing a potential conflict.