Doctors have been told to immediately stop immunising children under five after a spike in the number of West Australian youngsters experiencing fever and convulsions.
Health authorities are urgently investigating a possible cause.
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Australian Medical Association boss Andrew Pesce backed quality control processes used to test the vaccine, saying it remained safe for anyone aged over five.
"It's not possible to say why this has happened in WA," he told Sky News on Saturday.
"We need to wait for all the information to come in, but the public can be reassured vaccines are adequately clinically trialled when they are developed."
No other states have experienced a similar spike.
It was possible this was simply a "bad batch" but Dr Pesce was confident authorities will get to the bottom of the issue.
He urged those aged over five to go ahead with vaccinations.
