Companies such as Kraft, Kellogg and General Mills worked together to launch the "Smart Choices" program earlier this year. The program labels appear on the front of foods that meet certain nutritional standards.
The Food and Drug Administration said earlier this week such programs may be misleading consumers about the health benefits of certain foods. Smart Choices has been criticized because its guidelines allow cereals high in sugar to bear the stamp.
Manufacturers that currently use the logo can continue to do so.