Parents who do not vaccinate their children will lose welfare payments of up to $2100 per child under a federal government policy set to be announced before the May budget.

Under changes that could save more than $50 million a year, Social Services Minister Scott Morrison is preparing to scrap a "conscientious objection" provision which allows anti-vaccination parents to still claim welfare benefits including childcare assistance and Family Tax Benefit A.

Fairfax Media understands the Family Tax Benefit A is worth up to $2100 per child.

Parents of about 39,000 children have signed "conscientious objection" forms that certify they have a "personal, philosophical, religious or medical" objection to immunisation. This form, which requires a consultation with a doctor or immunisation nurse, is necessary for the parents to receive Family Tax Benfit A. But access is means tested so not every one of those parents would be receiving the payment.