GE Free NZ's complaint was heard last week by Parliament's regulations review committee.
Ms Kaye said she was confident in the approval process.
She noted that 57 GM varieties were already imported to New Zealand and Australia, which shared standards for food labelling and composition.
GE Free NZ said previous GM applications had used animal testing to show the product would be safe for human consumption. In this instance, Ms Bleakley claimed that testing agencies had relied on data provided by the applicant and not on animal tests.
"We believe that we should be feeding them to animals, specifically small rodents, on a long-term feeding study."
In its submission, GE Free NZ cited a Brazilian study in which transgenic soybeans had provoked an allergic reaction in some subjects.
The minister said New Zealand was able to opt out of approving a product if it had serious safety concerns.
"The recommendation I had from [the Ministry for Primary Industries] was not to review approval of this genetically modified food.
"This soybean has been assessed and presents no threat or risk to human health. I accepted that recommendation," Ms Kaye said.
The committee will consider the complaint by GE Free NZ. It can recommend to the House that a regulation be disallowed.