Australia's chief medical officer Jim Bishop today said health professionals should stop immunising children under five-years-old with the vaccine immediately.

The advice follows concerns the vaccine is adversely affecting children's health.

"We suggest doctors and health professionals vaccinating children don't use the seasonal flu vaccine for the moment, until we can get the Therapeutic Goods Administration (TGA) to investigate this in more detail,'' Professor Jim Bishop told ABC TV.

He said the concerns stemmed from a significant rise in the number of children developing a fever after receiving the vaccine.

"This is a precautionary measure while the matter is being urgently investigated by health experts and the Therapeutic Goods Administration (TGA),'' he said.

The drug regulator is trying to establish whether the bad reactions reported in WA are related to the vaccine, or whether there is a problem with how it is administered.

Prof Bishop said the TGA had contacted vaccine manufacturer CSL to identify which batches of the medicine had been sent to WA, and get samples of them for testing.

"The TGA is convening an expert scientific advisory panel to review the information from WA, and is seeking additional information from the manufacturer, CSL Ltd, and from regulatory colleagues internationally,'' he said.

The Department of Health and Ageing is also conducting its own inquiries into the issue, and states and territories are being encouraged to report any cases of fever or convulsion following the immunisation to the TGA.

Prof Bishop said those over the age of five could still receive the seasonal swine flu vaccine, while the swine flu shot was still safe for everyone - including children - to use, too.

"It is expected that the dominant flu this winter season will be swine flu and the specific Panvax vaccine is available free for all Australians,'' he said.

Western Australian Health Minister Kim Hames today suspended the state's free flu vaccination program for children under five, after some recipients went into a febrile convulsion - a fit caused by a high temperature.

Princess Margaret Hospital figures showed about 22 children had been brought to the hospital following febrile convulsions possibly linked to the vaccine in the past month.

Dr Hames said it was unclear if the fevers were related to the influenza vaccination but the precautionary measure was the most responsible course of action.

Fevers in the most instance are treatable.

"We need more information about what's happened in WA, but also what we can now find out from all the other states from their experience,'' Professor Bishop said.

"If this has been brought up as a possible side-effect of this drug, then we ought to at least suspend its use until we know more.''