The panel spent Friday debating the Covid-19 vaccine, which has for the past several years been a routine recommendation, like the yearly flu jab.
Acip voted to abandon broad support for recommending the jab, including for high-risk populations like people aged over 65.
Instead it decided they could make their own decision after talking with a medical professional.
In May, the federal government stopped recommending Covid-19 vaccines for healthy pregnant women and children.
In one exchange on Friday, Kennedy’s ally Dr Robert Malone argued there was no evidence that the Covid vaccine prevented serious infection.
Dr Cody Meissner, once part of the Food and Drug Administration’s vaccines panel, argued there is “pretty well-defined” data that the jab protects against infection.
There was confusion during the debate over the MMRV vaccine – measles, mumps and rubella, and varicella (commonly known as chickenpox).
On Thursday, the panel voted against recommending the combined MMRV shot for children aged four and under.
But on Friday they decided to endorse two separate jabs – a combined one for measles, mumps and rubella, and another for varicella.
The American Medical Association, which represents doctors and medical students, said the new MMRV recommendations “leave parents confused”.