WASHINGTON — The Centers for Disease Control and Prevention is facing renewed scrutiny over its handling of two measles deaths in Pennsylvania, with public health experts warning that the dispute could weaken cooperation between state and federal health officials at a dangerous moment for infectious disease response. The deaths were initially attributed to measles by Pennsylvania officials. Health and Human Services Secretary Robert F. Kennedy Jr. later questioned those findings, and the CDC removed the deaths from its website. The unusual public disagreement has raised concerns about whether political pressure is influencing federal disease reporting. Under the usual process, state health authorities investigate deaths and report their findings to the CDC. The federal agency generally relies on those state determinations when publishing national health data and issuing guidance to doctors, local health departments and the public. The controversy comes as the United States experiences its worst measles resurgence in decades. Vaccination rates have also declined, while seasonal flu, COVID-19 and respiratory syncytial virus remain recurring threats. “Red flag. Red alert,” said Dr. Demetre Daskalakis, who resigned last year as director of the CDC’s National Center for Immunization and Respiratory Diseases. Daskalakis said he left to protest what he described as political interference at the agency. “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.” Public health officials say the disagreement could damage the trust needed for states and federal agencies to share information quickly during outbreaks. Anne Zink, a senior fellow at the Yale School of Public Health and a former Alaska chief medical officer, described the relationship as increasingly strained. “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. “These partnerships are critical and essential to making us healthy and well.” The concern extends beyond measles. Officials and medical professionals depend on federal data to track flu, COVID-19 and RSV, determine where resources are needed and advise families about prevention. Georges Benjamin, executive director of the American Public Health Association, said uncertainty over national data could leave people unsure where to turn for reliable guidance. “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 dispute is also testing the leadership of CDC Director Dr. Erica Schwartz, who recently took over after a turbulent year marked by staff cuts and low morale. Some former agency officials had hoped Schwartz would rebuild the CDC’s credibility and resist political pressure. Daskalakis accused the agency of enabling conduct that conflicts with established public health science. Debra Houry, who resigned as the CDC’s chief medical officer alongside Daskalakis, said the director should be focused publicly on responding to the measles outbreak and encouraging childhood vaccination as students return to school. “I haven’t heard from her talking about the importance of getting kindergarteners vaccinated when we’re seeing declining rates,” 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 responded to repeated requests for comment. The immediate stakes are local as well as national: If families, doctors and health departments cannot trust official case counts and death reports, public health responses can become slower, less coordinated and less effective.