Public health experts found that young children were more likely to end up in hospital because of side effects from a flu vaccine than they were from the disease itself.
The analysis contradicts government safety advice that the harm did not outweigh the risk and raises concerns about the Therapeutic Goods Administration's assessment of the vaccine.
More than 1000 adverse responses in children under five were reported to the TGA by June this year, including nearly 100 instances of febrile convulsions, a seizure which in a small number of cases has been associated with long-term adverse health outcomes.
In the face of criticism over the three months it took to clearly identify CSL's Fluvax vaccine as the likely culprit, the federal health department sought to put some blame on the West Australian health department.
A spokeswoman for the federal department said WA health officials were aware of the side effects with the flu vaccine three weeks before they provided data to the Therapeutic Goods Administration about the reported febrile convulsions. ''This is the responsibility of the WA health department and is of great concern,'' the spokeswoman said.
Research published in the journal Eurosurveillance showed Fluvax might have caused two to three hospital admissions due to seizure for every admission from flu it prevented.
The chief executive of the Public Health Association of Australia, Michael Moore, said further examination of risks was needed, at arm's length from the TGA. The government should consider creating an independent centre.
"There is a concern … that the TGA is the body that approves vaccines and is also the body that determines what the risks and benefits are when concerns are raised," he said.
Peter Collignon, an infectious diseases expert at the Australian National University, said the vaccination program in children under five did more harm than good. "The TGA made that decision [about risk-benefit] without any evidence to back it up."
Professor Collignon questioned the TGA's independence and transparency because some of its advisers had worked for drug companies.
Ultimately, 100 cases of febrile convulsions were reported nationally earlier this year, with 53 occurring in Western Australia which has a policy of influenza vaccinations for all infants.
The federal department suspended flu vaccinations for children under five in April and recommended on July 30 not to use CSL vaccines for those under five.
A report commissioned by the West Australian government found there was a ''slow response by this state and the Commonwealth to apparent emerging adverse events''. It also said it was ''disturbing'' that neither Western Australia nor the Commonwealth had implemented surveillance measures recommended by the World Health Organisation.
Vaccination specialists said yesterday the Fluvax experience highlighted the need for a unified, active surveillance scheme.