The High Court decision demonstrated laws and regulations drafted 15 years ago were "seriously deficient," he said.
The court's decision put New Zealand at odds with other regulators around the world, including United States, Australia, and Germany which consider organisms resulting from these breeding technologies were not genetically modified, he said.
"Not only does this decision put us behind other countries, it blocks our ability to innovate and reduces our options to respond scientifically to issues that affect our primary production."
Scion manufacturing and bioproducts general manager Elspeth MacRae said the two breeding technologies altered the genetic code of an organism without the introduction of foreign genetic material into the genome of the cell.
Such technologies were important for forestry which had long breeding cycles and provided the industry with a rapid response to increasingly important issues, she said.
The breeding techniques could be used to help prevent spread of wilding pines, increase climate change tolerance, improve wood quality and growth rates.
It could take many more years and less precision if traditional breeding methods were used, she said.
Scion spokeswoman Christl McMillan said Scion would not have to remove any trees grown from the new techniques.
"We haven't used these technologies in trees, but it does mean that its affects our research strategically.
"We cannot benefit from the speed and precision that biotechnology brings to tree breeding."
Sustainability Council executive director Simon Terry said the ruling was good news for food exporters supplying high value markets such as Europe which will "generally not tolerate any detectable level of GM content".
Green Party genetic engineering spokesman Steffan Browning said the High Court decision was a win for the primary sector.
"If the European Union prevents imports of GE [genetically engineered] food using these techniques, and we allow them to be used here, we would be putting market access for our exports at risk," he said.
However agricultural technology company Agcarm chief executive Graeme Peters said the judgment was another blow for scientists wanting to use the techniques to develop new species, generate export income, and protect the environment.