But Christian Science Australia spokeswoman Kay Stroud said her organisation was “very neutral on the subject of vaccination”.
Ms Stroud also told Fairfax Media that the church would be able to determine if individuals were joining only for the sake of vaccinations.
“We’re not silly,” she added.
Following the rise in objections to vaccinations – from just under one per cent to two over the past decade – Mr Abbott’s government hopes to boost immunisation under the system.
Families who elect not to vaccinate their children could lose thousands in welfare and tax benefits, with some estimating the costs as high as AUS$11,000