Federal Health Minister Greg Hunt says he is astonished by allegations some doctors have "stooped to the level of the anti-vaccination movement" by helping families get around compulsory vaccinations for their children.

Key points: One doctor under investigation for 12 months

One doctor under investigation for 12 months Hunt says GPs supporting anti-vax movement will be found

Hunt says GPs supporting anti-vax movement will be found AHPRA, medical board says thorough investigation takes time

The Victorian Health Department and the Australian Health Practitioner Regulation Agency (AHPRA) are investigating claims that three GPs are assisting families opposed to vaccinations.

Mr Hunt said if the doctors are found guilty, he hoped the regulator would impose the toughest penalties possible and added there would be "no sympathy at all" from the Government.

"I am astonished that any people who've been through medical degrees … would deign to stoop to the level of supporting the anti-vaccination movement," he said.

The Minister said he hoped these were isolated cases but warned "if there are other doctors out there preaching anti-vaccination positions, then we will find them".

"If it is accurate that there are registered doctors who are advocating an anti-vaccination position, then they will have the full force of the authorities come down on them," he said.

Victoria's Acting Health Minister, Martin Foley, said one of the doctors was referred to the federal regulator 12 months ago.

"We're very concerned that it has taken over a year for the investigation to … well we're not sure, it certainly hasn't been resolved," he said.

"And during that period of time continued reports about these practitioners keep coming in."

A spokesperson for AHPRA and the Medical Board of Australia defended how long the investigations had taken.

"When we are investigating a matter and it appears to be a case of professional misconduct, we must refer it to an independent tribunal for hearing and decision," they said.

"As part of this process, we need to make sure that our investigations are thorough, follow due process and that the evidence we present meets the evidentiary standards of the tribunal.

"We have improved our performance on timeliness, but we must balance this with the need to do a thorough job. We will keep working on this."

'Anti-vax messages will be fiercely dealt with'

But one of the Melbourne doctors accused of helping parents avoid immunising their children says what he is doing is "totally legal".

Doctor John Piesse said he was "not very comfortable" with having his life taken over by the investigation.

"I'm using now the immunisation status certificate letters of contraindication which are provided for in the legislation and I'm doing it according to revisions of the legislation," he said.

"So it's totally legal.

"There's no freedom of speech about vaccines. Anyone who takes a contrary view is attacked."

In Australia, doctors can apply for an exemption for their patients on approved medical grounds.

Federal Government records from 2015 showed about 30,000 kids - or about 1.34 per cent of Australian children - were granted "conscientious objection" status.

But conscientious objection is no longer accepted by the Government as a valid reason for forgoing vaccination.

Earlier this year, the Federal Government subjected some welfare payments to a 'no jab, no pay' policy as part of a push to ensure 95 per cent of children were vaccinated.

Similar no jab, no play policies have been introduced in Victoria and adopted by schools and childcare centres.

The film, Vaxxed: From Cover-up to Catastrophe, has been causing controversy by linking the measles-mumps-rubella vaccine to autism, which has been medically discredited.

"We know vaccinations save lives, they save kids' lives, and they protect our community. Any message that runs counter to that should be fiercely dealt with," Mr Foley said.

Under the National Immunisation Program, babies are vaccinated for whooping cough, hepatitis B, polio, diphtheria, as well as measles and mumps and other conditions.

School-aged children are offered vaccination against chicken pox and human papillomavirus, or HPV.

Earlier this month, a campaign was launched to give parents evidence-based information about immunisations to counter anti-vaccination critics.