An influential US medical journal is rejecting a call from the secretary of the Department of Health and Human Services, Robert F Kennedy Jr, to retract a large Danish study that found that aluminum ingredients in vaccines do not increase health risks for children, the journal’s editor told Reuters.

Kennedy has long promoted doubts about vaccines’ safety and efficacy, and as health secretary has upended the federal government’s process for recommending immunization. A recent media report said he has been considering whether to initiate a review of shots that contain aluminum, which he says are linked to autoimmune diseases and allergies.

The study, which was funded by the Danish government and published in July in the Annals of Internal Medicine, analyzed nationwide registry data for more than 1.2 million children over more than two decades. It did not find evidence that exposure to aluminum in vaccines had caused an increased risk for autoimmune, atopic or allergic, or neurodevelopmental disorders.

The work is by far the best available evidence on the question of the safety of aluminum in vaccines, said Adam Finn, a childhood vaccination expert in the UK and pediatrician at the University of Bristol, who was not involved in the study.

“It’s solid, [a] massive dataset and high-quality data,” he said.

Kennedy described the research as “a deceitful propaganda stunt by the pharmaceutical industry”, and said the scientists who authored it had “meticulously designed it not to find harm” in a detailed 1 August opinion piece on TrialSite News, an independent website focused on clinical research. He called on the journal to “immediately retract” the study.

“I see no reason for retraction,” Dr Christine Laine, editor in chief of the Annals of Internal Medicine and a professor of medicine at Thomas Jefferson University, said in an interview.

The journal plans to respond to criticism the article has received on its website, Laine said, but it does not intend to respond directly to Kennedy’s piece, which was not submitted to the journal.

The lead author of the study, Anders Peter Hviid, head of the epidemiology research department at the Statens Serum Institut in Denmark, defended the work in a response post to TrialSite. He wrote that none of the critiques put forward by Kennedy were substantive and he categorically denied any deceit as implied by the secretary.

“I am used to controversy around vaccine safety studies – especially those that relate to autism, but I have not been targeted by a political figurehead in this way before,” Hviid said in an emailed response to Reuters. “I have confidence in our work and in our ability to reply to the critiques of our study.”

Kennedy had a number of criticisms, including the lack of a control group, that the study deliberately excluded different groups of children to avoid showing a link between aluminum and childhood health conditions – including those with the highest levels of exposure – and that it did not include the raw data.

Hviid responded to the criticisms on TrialSite. He said some of the points were related to study design choices that were reasonable to discuss but refuted others, including that the study was designed not to find a link. In fact, he said, its design was based on a study led by Matthew Daley, a pediatrician at Kaiser Permanente Colorado, which did show a link, and which Kennedy cited in his article.

There was no control group because in Denmark only 2% of children were unvaccinated, which was too small for meaningful comparison, Hviid added. The data was available for researchers to analyze, but individual-level data was not released under Danish law, he said.

Other prominent vaccine skeptics including those at the antivaccine organization Kennedy previously ran, Children’s Health Defense, have similarly criticized the study on the Annals of Internal Medicine site.

TrialSite staff defended the study for its scale, data transparency and funding while acknowledging the limitations of its design, a view seconded by some outside scientists.

Laine said that while some of the issues Kennedy raised in his article may underscore acceptable limitations of the study, “they do not invalidate what they found, and there’s no evidence of scientific misconduct”.

An spokesperson for the Department of Health and Human Services said the department had “no further comment than what the secretary said”.