Obama made the remarks at the annual Partnership for a Healthier America Summit in Washington, D.C.
"We've got to make sure we don't let anybody take us back," she said, noting particularly the Trump administration's efforts to unwind her legacy program to improve nutrition for schoolchildren.
Perdue's argument last week was, "If kids aren't eating the food, and it's ending up in the trash, they aren't getting any nutrition -- thus undermining the intent of the program."
While she didn't mention Trump by name, Obama alluded to the new administration's efforts to unravel work that she and her husband, the former president, made.
"You want to talk about nanny state and government intervention, well, 'you just buy the food and be quiet and you don't need to know what is in it,'" the former first lady said. "That is essentially what a move like this is saying to you moms.
"If we want to make this country great, our kids need to be healthy."
The Trump administration also is ending Obama's "Let Girls Learn" program that offers educational opportunities for adolescent girls in developing countries.
Michelle Obama, who was a popular first lady for eight years, has long been critical of Trump dating back to the president's campaign, although neither her nor her husband has been overly critical in public since he was inaugurated in January. Friday, she said her words were not motivated by politics.
"It's not politics. It's parenting," she said.
When President Barack Obama was in the White House, the first lady led a campaign to end child obesity with her "Let's Move" initiative.
"Think about why someone is OK with your kids eating crap," Obama said Friday. "You have to stop and think -- Why don't we want kids to have good food at schools? What is wrong with you?"
Former President Bill Clinton also spoke at the event Friday, along with a handful of other celebrities.