Kennedy said the commission's report was a "clarion call to do something with utmost urgency to end this crisis" of increasing rates of childhood obesity, diabetes, cancer, mental health disorders, allergies and neurodevelopmental disorders like autism.
It did not call for specific regulatory changes or restrictions on pesticides used in farming, as some farm groups had feared, and instead said the chemicals should be further researched.
It echoed previous Kennedy statements that highly processed foods and additives are health risks and that the food industry is too influential in the crafting of public health recommendations like the Dietary Guidelines.
Speaking at a press conference, he said there was a consensus to prioritise what he called the ultra-processed food crisis.
The report also takes aim at the US childhood vaccination schedule, saying the number of vaccines children are recommended to receive is more than in many European countries.
It said the links between vaccines and chronic disease and the effects of vaccine injury should be studied.
Thursday's report outlining the causes was due this week and will be followed by policy prescriptions due in August.
US President Donald Trump signed an executive order in February establishing the Make America Healthy Again Commission to investigate chronic illness and deliver an action plan to fight childhood diseases.
The commission is jointly run by the US Department of Health and Human Services and the White House, with Kennedy serving as its chair and the Domestic Policy Council chief as executive director.
Agriculture Secretary Brooke Rollins and other cabinet members sit on it, as do federal health agency chiefs and senior White House officials.
Before the report's publication, farm lobby groups had warned that criticising specific farm practices could impede collaboration on the administration's health agenda and put food production at risk.
As next steps, the report called for enhanced surveillance and safety research into drugs and childhood health outcomes and clinical studies comparing whole-food to processed-food diets in children.
The report says that ultra-processed foods, which it describes as industrially-manufactured food products, are associated with poor health.
It cites infant formula as an ultra-processed food that is concerning, saying that parents are increasingly buying European brands.
