Leading medical groups in the United States have raised alarm after the Centers for Disease Control and Prevention (CDC) under President Donald Trump took the unprecedented step of cutting the number of vaccines it recommends for children.

Monday’s sweeping decision, which advances the agenda of Trump-appointed Secretary of Health Robert F Kennedy Jr, removes the recommendation for rotavirus, influenza, meningococcal disease and hepatitis A vaccines for children.

It comes as US vaccination rates have been slipping, and the rates of diseases that can be protected against with vaccines, such as measles and whooping cough, are rising across the country, according to government data.

“This decision protects children, respects families, and rebuilds trust in public health,” Kennedy said in a statement on Monday.

In response, the American Medical Association (AMA) said it was “deeply concerned by recent changes to the childhood immunisation schedule that affects the health and safety of millions of children”.

“Vaccination policy has long been guided by a rigorous, transparent scientific process grounded in decades of evidence showing that vaccines are safe, effective, and lifesaving,” Sandra Adamson Fryhofer, a doctor and AMA trustee, said in a statement posted on the group’s website.

She pointed out that major policy changes needed “careful review” and transparency, which are lacking in the CDD’s decision.

“When longstanding recommendations are altered without a robust, evidence-based process, it undermines public trust and puts children at unnecessary risk of preventable disease,” she said.

The change was effective immediately and carried out following the approval by another Trump appointee, CDC acting director Jim O’Neill, without the agency’s usual outside expert review.

The changes were made by political appointees, without any evidence that the current recommendations were harming children, Sean O’Leary, chair of the American Academy of Pediatrics, said.

“It’s so important that any decision about the US childhood vaccination schedule should be grounded in evidence, transparency and established scientific processes, not comparisons that overlook critical differences between countries or health systems,” he told journalists.

Protections against those diseases are only recommended for certain groups deemed high risk, or when doctors recommend them in what’s called “shared decision-making”, the new CDC guidance stated.

States, not the federal government, have the authority to require vaccinations for schoolchildren.

But CDC requirements often influence the state regulations, even as some states have begun creating their own alliances to counter the Trump administration’s guidance on vaccines.

Kennedy, the US health secretary, is a longtime vaccine sceptic.

In May, Kennedy announced that the CDC would no longer recommend COVID-19 vaccines for healthy children and pregnant women, a move immediately questioned by public health experts who saw no new data to justify the change.

In June, Kennedy fired an entire 17-member CDC vaccine advisory committee, later installing several of his own replacements, including multiple vaccine sceptics.

In August, he announced that the US is to cut funding for mRNA vaccine development, a move health experts say is “dangerous” and could make the US much more vulnerable to future outbreaks of respiratory viruses like COVID-19.

Kennedy in November also personally directed the CDC to abandon its position that vaccines do not cause autism, without supplying any new evidence to support the change.

Trump, reacting to the latest CDC decision on his Truth Social platform, said the new schedule is “far more reasonable” and “finally aligns the United States with other Developed Nations around the World”.