Parents may have the power to prevent their children in state care from being vaccinated if a Supreme Court appeal is successful on Wednesday, possibly setting a dangerous precedent in the child protection system.

A young Melbourne mother is fighting an order by the Children's Court compelling her children to be immunised while in the temporary care of the Department of Health and Human Services.

A young Melbourne mother is fighting a Children's Court ruling for her children to be immunised while in temporary state care.

Legal Aid, which is backing the woman's appeal, said the Supreme Court appeal to be heard on Wednesday would "clarify parental rights for many other families caught up in the child protection system".

The case will test whether the government and Children's Court can make "major decisions" about children while they are in temporary state care including schooling, religion and medical procedures.