The case centres on whether the Children's Court magistrate was empowered to order that the children be immunised while in temporary state care.
Victoria Legal Aid barrister John McLoughlin, acting for the parents, believes the magistrate overstretched his powers when he made the order.
"The order that was made went beyond the proper use of the powers," McLoughlin said.
"It involves the encroachment into the area of parental responsibilities."
McLoughlin argued the temporary nature of the order meant it could not make "irreversible decisions like immunisation" or impose conditions with long-term effects.
However, Ian Freckelton QC, for the department, argues the magistrate acted within his powers and the court was entitled under the law to act in the best interests of children.
Justice Osborn has invited the Human Rights Commissioner and Victorian attorney-general to intervene in the case.
He will deliver judgment on a date to be fixed.
- AAP