A Melbourne mum cradled her 20-year-old daughter as she told a rally of more than 150 anti-vaccine campaigners the shots made her daughter irreparably ill.

She'll soon turn 21, but Katy Rapley is the size of a small child and gets around in a pushchair after developing an undiagnosed neurological condition when she was two.

Her mum Leanne Sims believes it was the infanrix hexa vaccine "poisoned" and disabled her daughter.

"I came today to support freedom of choice," she told AAP.

"Offer the vaccines to the people that want them, don't force everybody to have them with your s****y laws, let people decide for themselves what they want to do for their family and their children."

Ms Sims was one of several speakers at an anti-vaccine rally in Melbourne's Flagstaff gardens against the government policies, including penalising families that don't vaccinate their children.

The rally was one of four to happen in capital cities across the country on Sunday.

Other speakers accused the Victorian government's Better Health Channel website of giving false advice on measles, said vaccines were destroying heard immunity and that childhood diseases were once a "right of passage" and would have eventually died out if society left them alone.

The group also did a piece where participants held up signs with the number of vaccinations each generation must take to be fully covered and then linked the increase in shots to rising autism rates.

Following the rally, the group then marched to the Bourke Street Mall chanting "where there is risk there must be choice".

Acting Victorian Health Minister Martin Foley said the science was "crystal clear" and vaccinations saved lives.

"We make no apologies for making sure as many children as possible are immunised against serious and possibly life threatening diseases," he said in a statement.