It said processed food, chemicals, stress and overprescription of medications and vaccines may be factors behind chronic illness in American children, citing some 500 research studies as evidence.
Digital news outlet NOTUS reported the citation errors, saying it found seven studies listed in the report's footnotes that did not exist, along with broken links and misstated conclusions.
White House spokesperson Karoline Leavitt told reporters that any citation errors were due to "formatting issues."
The government said it posted a corrected version of the report later on Thursday.
"The substance of the MAHA report remains the same - a historic and transformative assessment by the federal government to understand the chronic disease epidemic afflicting our nation's children," the Department of Health and Human Services said.
Katherine Keyes, an epidemiology professor at the Columbia University Mailman School of Public Health, was cited in the report as the author of "Changes in mental health and substance use among US adolescents during the COVID-19 pandemic," which the report said was published in the medical journal JAMA Pediatrics.
She said neither she nor the named co-authors of the paper had written it.
"It does make me concerned given that citation practices are an important part of conducting and reporting rigorous science," she said.
Psychiatry Professor Robert L. Findling did not author the article cited in the report as "Direct-to-consumer advertising of psychotropic medications for youth: A growing concern" in the Journal of Child and Adolescent Psychopharmacology, according to a spokesperson for Virginia Commonwealth University, where Findling is a professor.
Kennedy Jr has spent decades sowing doubt about the safety of vaccines, raising concerns within the scientific and medical communities over the policies he would pursue as health secretary.
Since taking the role, he has fired thousands of workers at federal health agencies and cut billions of dollars from US biomedical research spending.
The studies attributed to Findling and Keyes no longer appeared in the MAHA report on the White House website as of Thursday evening.
