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 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. Health Secretary Robert F. Kennedy Jr. took to social media to claim the discrepancy meant the cases “may even have been altogether 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.

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.

Dr. Diamantoni said the clinic that treated the child did not refer the case to the coroner because the death was not unexpected: children with this genetic condition typically die within months, often because of a viral illness.

State health officials have not confirmed whether the six week old was one of the two deaths that they announced last week.

Dr. Diamantoni has maintained that measles did not contribute to the death of the first child, the newborn, who tested positive for measles and whose immediate cause of death was a lacerated spleen. State health officials have described the case as a “measles-associated death,” since the spleen can become enlarged in response to a measles infection, making it more vulnerable to injury and rupture.

As of Friday, the C.D.C.’s website still included a disclaimer that the agency would not include the deaths reported by the Pennsylvania Department of Health while the agency “reviews additional information regarding the circumstances and causes of death.”