Robert F Kennedy Jr, a vaccine critic who has pledged to tackle chronic disease, was named US Health Secretary on Thursday after overcoming resistance from the medical establishment and members of Congress with promises to limit his role in vaccination policy.

As Kennedy was sworn into the post, US President Donald Trump signed an executive order to establish a commission to "Make America Healthy Again," that would investigate chronic illness and deliver an action plan to fight childhood diseases.

Kennedy said on Thursday his first priorities would be around "radical transparency" and removing those in the government who had conflicts of interest.

"For 20 years, I've gotten up every morning on my knees and prayed that God would put me in a position where I could end the childhood chronic disease epidemic in this country. On August 23 of last year, God sent me President Trump," Kennedy said, referring to when he dropped his independent presidential bid and endorsed the Republican candidate.

The US Senate earlier on Thursday voted to confirm Kennedy 52-48, with Senator Mitch McConnell of Kentucky the lone Republican joining all 47 Democrats to vote against Kennedy, who had made pledges to protect existing vaccination programmes in a bid to secure votes of hesitant lawmakers.

Kennedy will now oversee multiple high-profile agencies, including the Food and Drug Administration and Centers for Disease Control and Prevention.

Kennedy, 71, is an environmental lawyer who has long sown doubts about the safety and efficacy of vaccines that have helped curb disease and prevented millions of deaths for decades.

He will now run the Department of Health and Human Services (HHS) that directs more than US$3 trillion in healthcare spending.

Also under HHS purview are the Medicare and Medicaid programmes that provide health insurance for over 140 million Americans and the National Institutes of Health.

In addition to pledging to work to end chronic disease, Kennedy has said he wants to break any ties between employees at the US drugs regulator and industry. (Reuters)