The Obama administration is "very confident" that a surprise growth of genetically modified Oregon wheat that set off a trade dispute was an "isolated incident," according to Agriculture Secretary Tom VilsackThomas James VilsackUSDA: Farm-to-school programs help schools serve healthier meals OVERNIGHT MONEY: House poised to pass debt-ceiling bill MORE.

While he's not certain how the genetically modified strain, which is not approved for commercial growth, ended up in an Oregon wheat field, Vilsack said on Bloomberg Government's "Capitol Gains" that people should not be afraid of such strains sneaking into the food supply.

"Very confident that it did not and does not pose any threat to the food supply. And we’re now, obviously, working with our trading partners to assure them that we have the tests that they can conduct to assure their customers and consumers that the wheat is – is safe and is not in any way, shape, or form impacted or affected by this isolated incident."   

When the genetically modified strain was discovered, Japan announced a ban on American wheat, and the European Union began testing imports and seeking reassurances from the U.S.

Vilsack said he was hopeful those shipments to nations barring imports could resume soon.

"If we reassure our trading partners it's an isolated incident…we should see a resumption of full trade by all of our trading partners hopefully very soon," he said.

However, he still did not have an answer for how that wheat strain ended up being grown in the first place, saying the matter was still under investigation and the U.S. may never know exactly what happened.

"It may be a circumstance that it may be difficult at the end of the day to pinpoint exactly how this happened," he said.

On the farm bill, Vilsack continued to maintain pressure on Congress to pass legislation, while criticizing the House GOP bill that seeks to make steep cuts to food stamp programs, calling it "off the mark."

He also criticized the GOP approach to the farm bill. After failing to pass a measure that included food stamps, Republicans are seeking to split the bill, passing a bill with farm subsidies and another with food stamps. Vilsack warned that in the long run, this strategy could make it tougher to pass the farm bill and win over non-rural legislators.

"By having the food assistance programs in the bill, you basically have a good message point to suburban and urban legislators who may not fully understand what agriculture contributes to their constituents, and the likelihood is that you’re going to get that coalition of members in Congress to be able to pass a bill," he said.