Doctors are bracing for a fight as Australia's 12th national immunisation conference kicks off in Adelaide today.

They say they will address any legitimate concerns raised by anti-vaccine groups, but warn the risk of disease and death is much higher if parents do not have their children vaccinated.

Public health authorities say they are concerned by the rising number of children no longer immunised in particular pockets of Australia.

It comes as lobby groups argue that parents should get more information before they choose to vaccinate their child.

The chief executive of the Public Health Association (PHA), Michael Moore, says doctors are now trying to tackle the issue head on.

They are now formally debating whether they are too hard on the anti-vaccination lobby.

Mr Moore says two major reports have prompted the debate.

"The first of those was the New South Wales Health Care Complaints Commissioner who dealt with the anti-vaccination lobby and suggested that in many ways their website and their material is deceptive," he said.

"But on the other hand we had a report on August 9 from Professor Brian Stokes in Western Australia who dealt with adverse events that did occur with regards to seasonal influenza and actually had, right across Australia, young people under five years old not being given that vaccine."

In some ways, the PHA is perhaps playing devil's advocate to get doctors to argue that in fact they are too hard on the anti-vaccination lobby.

"What we're interested in was to try to make sure that we understand and that what comes out is the notion that the anti-vaccination lobby do have some points and actually we should deal with those," Mr Moore said.

"It's not actually reaching so much the lobby but the people who have real concerns about vaccination.

"I doubt if there's any parent when they're going to vaccinate their kids [who] doesn't give it a thought and go 'well, is this the right thing, or is this not the right thing?'"

Mr Moore says he hopes a more effective communication strategy will stem from the debate.

"So as parents are thinking about these things that people who understand immunisation can say 'What are your questions? What are your doubts?'"

"There are adverse incidents associated with immunisation, but in the end the decision is one of a cost benefit, or if you like, a risk analysis.

"It's actually much higher risk to not vaccinate your children than to vaccinate them."

The PHA says despite the pockets of low take-up of vaccinations, Australia still has the third highest rate of immunisation in the world.