Mr Kennedy’s exchanges with Democratic senators on the panel repeatedly turned to shouting, from both sides.
But some Republican senators also expressed unease with his changes to Covid-19 policies.
The Republican senators noted Mr Kennedy said US President Donald Trump deserved a Nobel Prize for the 2020 Operation Warp Speed initiative to quickly develop mRNA Covid-19 vaccines, but that he had also attacked the safety and continued use of these jabs.
“I can’t tell where you are on Operation Warp Speed,” said Republican North Carolina senator Thom Tillis.
Mr Tillis and others asked him why the director of the Centres for Disease Control and Prevention (CDC) was fired last week, less than a month into her tenure.
Mr Kennedy said she was dishonest, and that CDC leaders who left the agency last week in support of her deserved to be fired.
He also criticised CDC recommendations during the Covid pandemic tied to lockdowns and masking policies, and claimed – wrongly – that they “failed to do anything about the disease itself”.
“The people who at CDC who oversaw that process, who put masks on our children, who closed our schools, are the people who will be leaving,” Mr Kennedy said.
He later added that they deserved to be fired for not doing enough to control chronic disease.
The senate finance committee had called Mr Kennedy to a hearing about his plans to “Make America Healthy Again”, but Democratic senators pressed Mr Kennedy on his actions around vaccines.
Senator Ron Wyden of Oregon said Mr Kennedy had “stacked the deck” of a vaccines committee, replacing scientists with “sceptics and conspiracy theorists”.
He had tried to have Mr Kennedy formally sworn in as a witness, saying the health secretary had a history of lying to the committee.
The committee’s chair, senator Mike Crapo of Idaho, denied the request, saying “the bottom line is we will let the secretary make his own case”.
Last week, when the Trump administration fired the CDC’s director less than a month into her tenure, several top CDC leaders resigned in protest, leaving the agency in turmoil.
The ousted director, Susan Monarez, wrote in The Wall Street Journal on Thursday that Mr Kennedy was trying to weaken public health protections.
“I was told to preapprove the recommendations of a vaccine advisory panel newly filled with people who have publicly expressed anti-vaccine rhetoric,” Ms Monarez wrote.
“It is imperative that the panel’s recommendations aren’t rubber-stamped but instead are rigorously and scientifically reviewed before being accepted or rejected.”
Mr Kennedy told senators he did not make such an ultimatum, although he did concede that he ordered Ms Monarez to fire career CDC scientists.
Mr Kennedy pushed back on concerns raised by multiple Republican senators, two of whom are physicians.
He also repeatedly pushed back against Democrats.
In May, Mr Kennedy – a long-time leader in the anti-vaccine movement – announced Covid vaccines would no longer be recommended for healthy children and pregnant women, a move opposed by medical and public health groups.
In June, he abruptly fired a panel of experts that had been advising the government on vaccine policy. He replaced them with a handpicked group that included several vaccine sceptics, and then shut the door to several doctors groups that had long helped form the committee’s recommendations.
A number of medical groups say Mr Kennedy cannot be counted on to make decisions based on robust medical evidence.
In a statement on Wednesday, the Infectious Diseases Society of America and 20 other medical and public health organisations issued a joint statement calling on Mr Kennedy to resign.
“Our country needs leadership that will promote open, honest dialogue, not disregard decades of life-saving science, spread misinformation, reverse medical progress and decimate programmes that keep us safe,” the statement said.
Many of the nation’s leading public health and medical societies, including the American Medical Association, American Public Health Association and the American Academy of Paediatrics have decried Mr Kennedy’s policies and warned they will drive up rates of vaccine-preventable diseases.
