"Research suggests that the proliferation of divergent FOP approaches is likely to be confusing to consumers and ultimately counterproductive," Schneeman wrote.
But proponents of the Smart Choices label say the ranking system is valid.
"Our program is entirely transparent. The criteria have been published and available to all Americans," Richard Kahn, a Smart Choices board member and former chief scientific and medical officer for the American Diabetic Association, told ABC News. "The whole process took about two years to develop. The FDA was actually at the table at virtually all the meetings."
The board is open to a public review of the system and how it was developed, Kahn said, adding that it's built on a "solid scientific basis."
"It's not the perfect program but it's a program that's going to move America," he said. "There's nothing about these criteria that are not grounded in science."
Manufacturers say they will work with the FDA to research and develop a more helpful system.
"Our goal at Kraft Foods is to give consumers clear information," the company said in a statement. "That's why we support a common approach to front-of-package labeling. We look forward to continuing to work with FDA to help consumers make informed food choices."
The Grocery Manufacturers Association echoed similar sentiments.
"Manufacturers have already introduced or reformulated over 10,000 products to reduce calories, sugar, sodium, fat and trans fat or to enhance their nutritional profile, such as with the addition of whole grains or minerals," the association said in a statement. "This initiative, along with the many valuable programs and initiatives that are underway, can serve as another important step in improving the health and wellness of the American public."
General Mills declined to comment when contacted by ABC News, referring instead to the statement by the Smart Choices Program.
ABC News' Ben Krolowitz contributed to this report.