The Lancaster County coroner has determined that a six-week-old child in Pennsylvania died from measles. The child, who died last month, had a rare genetic disorder called Amish microcephaly, which can make a child vulnerable to respiratory infections, Dr. Stephen Diamantoni, the county coroner, said on Friday. Last week, state officials announced two measles deaths in Lancaster County, amid an expanding outbreak that has sickened 540 people and hospitalized more than 90.

Controversy broke out almost immediately after state officials made that announcement. Dr. Diamantoni said that he had only been referred one potential case, a newborn who tested positive for the virus and died shortly after childbirth. On social media, Health Secretary Robert F. Kennedy Jr. claimed the discrepancy meant the cases may have been “fabricated” by a staffer of the state’s Democratic governor, Josh Shapiro.

Dr. Erica Schwartz, the new director of the Centers for Disease Control and Prevention, instructed agency staff not to include the two deaths in the agency’s national measles count, breaking with the C.D.C.’s normal procedure of accepting the data reported by states. On Friday, the C.D.C. furthered escalated the fight, saying on its website that it does not have any records to indicate “measles is the underlying cause” of the deaths.

Dr. Diamantoni said in an interview that after the announcement by state officials, his office began an investigation to find out more information about the second case. He discovered the child with Amish microcephaly and said he felt confident that measles contributed to the death, based on a review of the child’s medical records. Lancaster Online, a local outlet in the county, was the first to report details of this death.