Priya, her husband Nadesalingam and their Australian-born children Kopika, 4, and Tharunicaa, 2, are being held on Christmas Island after a temporary injunction halted their deportation from Melbourne to Sri Lanka.

The family's legal battle centres on whether Tharunicaa should have had her case assessed by the minister.

"The two matters have now been combined together so will run as a Federal Court matter as opposed to a Federal Circuit Court matter and a Federal Court matter," family lawyer Carina Ford said outside court on Monday.

"The only other thing is that consent has been given to add the minister for home affairs as a party and the secretary of home affairs," she said.

On Monday, Federal Circuit Court Judge Heather Riley allowed for the case to be transferred to the Federal Court.

"It was really due to grounds and a jurisdictional issue whether or not they needed to be run in separate courts," Ms Ford said of the decision.

But even if the case is successful, the family's future in Australia will be decided by Home Affairs Minister Peter Dutton.

"The only way this family is going to stay, even if the court application is successful, is for the minister to intervene because he is the only one that holds that power," the lawyer said.

The current case does not change the circumstances for the family, who remain in detention on Christmas Island.

"This doesn't really change anything for the family at the minute as we all know the injunction is until 4pm on Wednesday," Ms Ford said.

The family had been in long-term immigration detention in Melbourne until Thursday night, when they were put on a plane for deportation to Sri Lanka.

But a judge issued a last-minute injunction and the family was taken off the plane when it landed in Darwin.

A court will hear the youngest child's case for Australia's protection on Wednesday.

Australian Associated Press