Centrelink says an “IT error” has led to parents being wrongly accused of not immunising their children, and denied payments.

The glitch has left many families without their Child Care Subsidy (CCS), even though their immunisations are up to date on the Australian Immunisation Register.

CCS is offered as a way to make childcare more affordable, offering varying amounts according to a family's income and working hours, but only if they vaccinate their children.

It mans affected families are paying full price for childcare until the problem is rectified. The authorities say families will be back paid, but the outlay is still too much for some.

“When they have to pay full fees, their budget goes completely out the window and [the problem] can go on for a significant period of time,” Australian Childcare vice president Nesha Oneil Hutchinson says.

“There are reports of families needing to withdraw their children until the subsidy starts flowing through … because they can't afford to cover those full fees until glitches in the system are ironed out.”

Services Australia is in charge of both Centrelink and the Australian Immunisation Register, but will not say how many people were affected.

“There are no ongoing issues and it was not widespread,” Services Australia general manager Hank Jongen said.

Media report say there are many examples of cases yet to be resolved.