President Donald Trump on Monday signed an executive order directing the federal government to pursue significant changes to the nation’s childhood vaccination recommendations, including separating combination vaccines and spacing out shots over multiple medical visits.

The order calls for the measles, mumps and rubella, or MMR, vaccine to be administered as three separate shots when individual vaccines become available in the United States. It also recommends that, to the greatest extent feasible, childhood immunizations be administered at separate medical appointments rather than together.

In a statement, the White House said the order is intended to promote greater parental choice and improve vaccine research. It directs the Department of Health and Human Services to reassess the timing and sequencing of childhood vaccines and advance additional research into vaccines and autism.

The move represents a major shift in federal vaccine policy and comes as the school year begins in many parts of the country and the United States faces a significant measles outbreak.

Trump has for years questioned whether the number and timing of childhood vaccinations could contribute to autism. Those concerns have persisted despite decades of research and a broad scientific consensus that vaccines do not cause autism. Studies have examined both individual vaccines and the effects of receiving multiple vaccines according to recommended schedules.

The order follows months of debate within the Trump administration over childhood immunizations. Health Secretary Robert F. Kennedy Jr., who has a long history of questioning vaccine policies, has pushed for changes to the federal vaccination schedule. Vaccine advisers appointed by Kennedy previously recommended separating the MMR vaccine into individual shots.

The administration’s actions also follow an earlier effort to reduce the number of vaccines recommended for children. The Centers for Disease Control and Prevention in January recommended reducing the number of childhood vaccinations for certain diseases, while the American Academy of Pediatrics maintained recommendations covering a broader range of childhood diseases. A federal judge later blocked the CDC’s proposed changes.

The executive order does not itself eliminate state vaccination requirements for students. States continue to determine which vaccines children must receive to attend public schools, although federal recommendations can influence medical practice, insurance coverage and public health policy.

One of the most consequential changes proposed by the order involves the MMR vaccine. The combined vaccine protects children against measles, mumps and rubella with a single series of shots. Separate measles, mumps and rubella vaccines are not currently available for children in the United States, meaning the administration’s recommendation would depend on the availability of individual vaccines.

Medical experts have raised concerns that requiring additional appointments could make it more difficult for children to receive all recommended doses. More appointments create additional opportunities for missed visits or delayed vaccinations, potentially increasing the period during which children remain unprotected.

Although recommendations from the C.D.C. greatly influence state regulations, states, not the federal government, have the authority to mandate vaccinations.