Critics saw in the move the beginnings of a more restrictive approach to providing vaccines to Americans.

An advisory panel recently appointed by Health Secretary Robert F. Kennedy Jr. voted on Thursday to walk back longstanding recommendations for flu vaccines containing an ingredient that the anti-vaccine movement has falsely linked to autism.

The vote signaled a powerful shift in the way federal officials approach vaccines, putting into action Mr. Kennedy’s deep skepticism about their safety and delivering the first blows to a scientific process that for decades has provided effective vaccines to Americans.

Mr. Kennedy fired all 17 experts on the panel about two weeks ago, and then appointed eight new members, at least half of whom have expressed skepticism about some vaccines.

“We came to this meeting with no predetermined ideas, and will make judgments as if we are treating for our own families,” the panelists said in a statement.

To critics, the two-day meeting of the Advisory Committee on Immunization Practices offered the clearest signs yet that the Trump administration intends to unravel the system that has long guided clinical decisions about vaccination.

“As a physician and scientist who has devoted my entire career to vaccines and preventing and treating infections, this meeting has been devastating to watch,” said Dr. Lakshmi Panagiotakopoulos, an expert on vaccines who resigned from the Centers for Disease Control and Prevention earlier this month.