PUBLIC health experts have called for an independent body to monitor drug safety after it emerged 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.

The side effects were linked to one of the three seasonal flu vaccines, Fluvax and Fluvax junior, from the drug company CSL, but the TGA maintained despite that, that "the overall risk-benefit balance of both products remains positive".

The Commonwealth Chief Medical Officer claims the advice was intended to indicate the drug should not be withdrawn from the market but said the government would reassess it in light of the research.