Flanked by Health Secretary Robert F Kennedy Jr, the US president baselessly linked autism to the use of paracetamol by pregnant women and childhood vaccines.
Health Minister Mark Butler said he was "really worried" the comments would leave more than 200,000 pregnant Australian women unsure or afraid of what to do when they become sick, particularly with fever.
"I don't want pregnant women right now to feel unsure about what to do," he told Nine's Today on Wednesday.
"I don't want women who were pregnant in the past to feel unsure or even guilty about the fact that they took a treatment that was advised to them as being safe."
The Therapeutic Goods Administration on Tuesday joined other medicines regulators, leading clinicians and scientists worldwide in declaring "robust scientific evidence" showed no causal link between the use of paracetamol in pregnancy and autism or ADHD.
"Paracetamol remains the recommended treatment option for pain or fever in pregnant women when used as directed," it said.
"The TGA has no current active safety investigations for paracetamol and autism, or paracetamol and neurodevelopmental disorders more broadly."
In the White House media event, Mr Trump relied on personal feelings and an anecdote to suggest changes to the US's longstanding, evidence-based vaccination schedule for children.
Mr Butler said the Republican president's remarks about combination jabs such as the measles, mumps and rubella vaccine were the "most worrying aspect" of the press conference.
"I do not want further uncertainty about the importance our childhood immunisation program at a time when, like the rest of the world, frankly, after COVID, rates of childhood immunisation are going the wrong way," he said.
Child psychologist Tanya Forster, whose six-year-old boy has autism, said the claims from the Trump administration would create a lot of anxiety for families.
"We have worked so hard to increase awareness and to break down stigma, to encourage families to reach out and to seek support," she said.
"To make such a declaration in a position like that on a world stage really is a setback for the work that we've done."
A parenting expert and the chief executive of Macquarie Health Collective, Ms Forster fears some parents may believe Mr Trump and worry that they caused their children's autism, leading to potential self-criticism and blame.
"That's something that parents struggle with enough," she said.
Mr Trump's assertions were unfounded and could cause distress and confusion in the community, the Australian Association of Psychologists says.
"These unsubstantiated claims seem to be placing the blame on parents for taking an everyday medication that has proven to be safe," the association's chief services officer Amanda Curran said.Â
"Autism is a neurodevelopmental difference, not a disease or deficit to be feared or prevented."
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