Parents whose children don't meet immunisation requirements will have their welfare payments docked $28 a fortnight after legislation cleared parliament.
Under the federal government's tougher "no jab, no pay" policy, fortnightly Family Tax Benefit Part A payments will be reduced from July 1 for each child who has not been vaccinated.
The legislation, which passed the Senate on Wednesday, replaces the existing system under which end-of-year supplements are withheld for children whose immunisations are not up to date.
Government minister Concetta Fierravanti-Wells said the policy had already achieved significant increases in immunisation rates.
"The new measure will serve as an immediate incentive and constant reminder for non-compliant parents," Senator Fierravanti-Wells told parliament.
Labor senator Louise Pratt said the more immediate penalties would help stop anti-vaccination beliefs from gaining a foothold in communities.
"We need to rely on strong herd immunity through vaccination and ensuring that people receive adequate vaccination," she said.
The bill also makes changes to child support payments, some of which were opposed by Labor and the Greens.
Senator Pratt said changes to parents' payments could be applied retrospectively, raising concerns people would be forced to pay back money they had already spent.
Greens senator Rachel Siewert warned parents, including single mothers, would have harsher debt recovery measures used against them even when administrative errors were made.
"If overpayment to payees is in fact such a significant issue, it should not be addressed through such a sledgehammer approach," she said.
But Senator Fierravanti-Wells said the measures would not create new debt and allow over- and under-payments to be identified earlier.
"The debt already exists whether this measure passes or not," she said.
The opposition's attempt to have the debt recovery measure cut out of the bill failed.