ATLANTA — The Centers for Disease Control and Prevention is facing renewed scrutiny after it removed two Pennsylvania measles deaths from its website following public questions from Health and Human Services Secretary Robert F. Kennedy Jr. Pennsylvania health officials had attributed the deaths to measles, but Kennedy challenged that determination. The CDC then took the unusual step of removing the cases from its public data, prompting former federal health officials and outside experts to question whether political considerations are influencing disease reporting. The dispute comes as the United States confronts its worst measles resurgence in decades. Vaccination rates have continued to fall, while flu, COVID-19 and RSV are expected to return with the approaching respiratory-virus season. Dr. Demetre Daskalakis, who resigned last year as director of the CDC’s National Center for Immunization and Respiratory Diseases, called the episode a “red flag” and a “red alert.” Daskalakis said the federal government’s decision to question a state’s determination of cause of death could damage the system used to warn doctors, health departments and the public about infectious-disease threats. “When they raise doubt on the adjudication that a state may have made around a death, that is highly problematic,” Daskalakis said. “This is dangerous.” States typically investigate deaths within their jurisdictions and report their findings to the CDC. The federal agency generally relies on those state determinations as it compiles national health statistics and issues public warnings. Anne Zink, a senior fellow at the Yale School of Public Health and a former Alaska chief medical officer, said the Pennsylvania dispute reflects a broader breakdown in cooperation between state and federal health authorities under the Trump administration. “What we have been seeing, that got amplified even more with these measles cases, is a breakdown in the coordination and trust between states and the federal government,” Zink said. She warned that those partnerships are essential to protecting the public. Public-health leaders are now questioning whether similar pressure could affect federal data on flu, COVID-19 or RSV. Georges Benjamin, executive director of the American Public Health Association, said national health information must remain grounded in evidence rather than political messaging. “We need to have good solid evidence-based national data,” Benjamin said. “If it happens with flu and with COVID, the question is: Who can we rely on for the data on a national level?” The controversy also puts pressure on CDC Director Erica Schwartz, who recently took over after a turbulent year marked by staff cuts and declining morale. Some public-health veterans had hoped Schwartz would rebuild the agency’s credibility and resist political interference. Daskalakis accused the agency of facilitating what he called “non-scientific behavior,” while Debra Houry, who resigned as the CDC’s chief medical officer alongside Daskalakis, said the director should be focused on stopping the outbreak rather than disputing disease counts. “It’s back to school time around the United States,” Houry said. “We need her to step up publicly to talk about what can be done.” Neither the CDC nor the Department of Health and Human Services provided a response to repeated requests for comment. For communities preparing for another season of contagious respiratory illnesses, the immediate concern is not merely the number of cases reported by Washington, but whether families, doctors and local officials can trust the numbers at all.