Mr. Perdue said the Obama-era rules had resulted in increased costs for school districts and declining participation in the federal school lunch program. He said relaxing the rules was part of the administration’s effort to “make school meals great again.”

“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,” said Mr. Perdue, who announced the changes with a signed proclamation on Monday after having lunch with students at Catoctin Elementary School in Leesburg, Va. Mr. Perdue, a former governor of Georgia, was just confirmed last week.

Nutrition advocates said the move by the Trump administration was shortsighted.

“Just because children would rather eat heavily salted, processed foods at school doesn’t mean they should,” said Ken Cook, president of the Environmental Working Group. “The president’s fondness for Big Macs and KFC is well known, but we shouldn’t let Colonel Sanders and McDonald’s run the school cafeteria.”

Since schools began complying with the nutrition standards in 2012, many have complained that they are too stringent and costly. The new rules were projected to cost $3.2 billion over five years, but Mr. Perdue said they had cost states an additional $1.22 billion in the 2015 fiscal year alone.

Congress has allowed states to apply for waivers if they cannot meet certain standards.

Nancy Brown, chief executive of the American Heart Association, said in a statement that schools were moving forward to meet the requirements. The organization denounced the Agriculture Department’s relaxation of the rules, noting that more sodium and sugar would increase students’ blood pressure and put them at greater risk of heart disease and strokes.