University of Sydney researchers have established a link between influenza and "devastating" brain diseases in children.

Influenza has been linked to a deadly brain disease in Australian children, prompting calls for a universal flu vaccination program for the very young.

During the past three flu seasons, 54 cases of potentially fatal influenza associated neurological disease (IAND) were recorded among children aged up to 16 at two Australian hospitals, according to a University of Sydney study published in the journal Clinical Infectious Diseases.

This represents 7.6 per cent of the 710 children admitted to hospital with the flu during this period.

Of the 54 cases of IAND, 10 children became critically ill with influenza associated encephalitis (IAE), two of whom died, three suffered permanent brain damage and six were admitted to an intensive care unit.

Encephalitis is a sudden onset inflammation of the brain due to infection.

According to the authors, the incidence of IAE was comparable to that during the 2009-2010 flu pandemic and in East Asian populations.

"These findings support the case for universal influenza vaccination in young children," the authors wrote.

Lead researcher Dr Philip Britton says there is an "under appreciation" among the community and even health practitioners about how severe flu can be.

"As a result flu immunisation for children is significantly underdone in our community," Dr Britton told AAP.

Children with pre-existing neurological conditions, such as epilepsy, were found to be at heightened risk.

The other group at heightened risk were previously healthy children with no known risk factor.

"Even children under the age of five who are previously well can die or end up with brain damage from flu," warned Dr Britton.

It's thought this likely stems from a genetic predisposition, however the researchers at yet to prove that.

These conditions are rare yet burdensome and can be avoided through the influenza vaccine, says Dr Britton.

"In this care, prevention is better than treatment," he said.

"Although infrequent, because of how severe the disease is it's worth looking at that in more detail and incorporating that into the kind of cost benefit analyses that go into deciding whether you are going to fund a vaccine at a population level," Dr Britton said.