For instance, they point to the typical language in the letters the agency sends to companies at the end of the evaluation that seems to say the conclusion on safety is that of the company, not the agency. For example, the letter to Okanagan says, “It is our understanding” that Okanagan “has concluded” that the apples are not materially different in safety and nutrition from other apples.

But the F.D.A. said on Friday that its evaluations were thorough.

“The consultation process includes a review of information provided by a company about the nature of the molecular changes and the nutritional composition of the food compared to traditionally bred varieties,” Dennis Keefe, director of the agency’s office of food additive safety, said in a statement. “This case-by-case safety evaluation ensures that food safety issues are resolved prior to commercial distribution.”

The F.D.A. told both Okanagan and Simplot that certain differences between the genetically engineered apples and potatoes and conventional ones might be material enough to require disclosure to consumers. It urged the companies to consult further with the agency about voluntary or required labeling.

Such labeling would refer to the traits like resistance to browning or the lower amounts of the suspected carcinogen in fried potatoes, said Theresa Eisenman, an F.D.A. spokeswoman. It normally would not refer to the fact that the crops were genetically engineered, she said. However, the agency has received petitions on this matter and is considering them.

Doug Cole, a spokesman for Simplot, said the company would sell seed to growers, so it would not be responsible for how the potatoes or products containing those potatoes would be labeled. But he said the company would urge growers and retailers to label the benefits — less bruising, for example — just as is done with seedless watermelons.