"They are unable to really compete," Director Miriam Mayet says.
For the moment, such concerns are confined to South Africa, the continent's only country where GM seeds are commercially planted. (Many nations, like Malawi, won't even accept GM crops in their food aid shipments.)
But many of Africa's less food-secure countries are cozying up to the technology.
Consider Uganda: That's where humanity first domesticated the banana, delivering Africa's first great agricultural revolution.
Now, Uganda's Agricultural Research Center is tinkering with the millennia-old staple crop to pack more nutrients under its peal.
Nearby Tanzania is launching new field trials for Bt Cotton, which it says could triple its cotton yield.
"There are a whole host of other food crops which are now receiving attention for research and development," he says. "This is technology that can help poor farmers."
The European Union maintains a de-facto ban on GM foods.
In America, the seeds are blamed for sprouting a crop monoculture, where whole once-sundry states have been reduced to sprawling cookie-cutter corn fields, and everything from apples to gas tanks to your soda-slupring stomach is coated in corn.