Justices say the facts of the case – in terms of any breach of duty of care towards the girl – need to be determined first

The federal court has stymied the government’s attempt to challenge its jurisdiction to order that sick asylum seekers and refugees be brought to Australia.

Lawyers for the Department of Home Affairs pushed for the hearing as part of an undertaking they gave last month to bring a gravely ill 11-year-old girl from Nauru to Australia for urgent medical treatment.

They sought to argue that the federal court did not have jurisdiction to order that asylum seekers or refugees be brought to Australia, because of a 2015 legislative amendment that banned legal proceedings on matters relating to regional processing centres.

Instead, they argued, those cases would have to be determined by the high court.

That outcome could void previous federal court orders to bring people to Australia for medical care and remove the federal court as a lifeline for refugees and asylum seekers on Manus Island and Nauru.

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The department was prepared to argue the matter before the full bench of the federal court in Melbourne on Friday, one day after the government signalled that it was prepared to remove the remaining 38 children from Nauru by the end of the year.

But in a joint order, justices Alan Robertson, Susan Kenny, and John Griffiths said it was not appropriate to test the jurisdictional issue as a separate question until the facts of the case — that is if, how, and by what means the government had breached its duty of care towards the girl — were known or at least substantially agreed.

The order does not prevent the department from challenging the federal court’s jurisdiction at a later stage in this case, or in another case where an urgent medical transfer is sought.

The girl is being represented by the Human Rights Law Centre (HRLC) and private firm Robinson Gill lawyers.

“For now, desperately unwell people being mistreated by the government on Manus or Nauru can still take their case to the federal court,” HRLC director of legal advocacy Daniel Webb said.

“The government has never raised this argument in any of our previous cases – time will tell if they try it again.”

Lawyers for the department had said the jurisdictional question should be argued as a test case, and that it would affect several other cases that would soon be before the court.

But the court heard that many of the people subject to those cases had since been transferred to Australia — among the 135 people who have been brought to the country from Nauru since 15 October.

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The justices ruled that the girl’s case was no longer an appropriate test case because she and her family had already been brought to Australia and she was now receiving medical treatment, meaning any decision relating to her case would not be applicable to cases where an urgent transfer from Nauru was required.

They also suggested that setting a general bar against legal proceedings in this case might not succeed because it depended on the legal basis on which lawyers for the girl had claimed the government had breached its duty of care.

“The issue of jurisdiction may therefore need to be determined more than once,” Griffiths said.

Ninety people have been brought to Australia on federal court orders that could be voided if the federal government’s argument is successful. Another 240 people have been transferred after legal proceedings were threatened or launched.

The girl arrived in Australia with her family from Iran in 2013 and was moved to the regional processing centre on Nauru in 2014. They have all since been granted refugee status on Nauru and lived in the community.

She was brought to Australia along with her parents and two siblings on 21 October, three days after her lawyers filed a negligence suit on her behalf.

The negligence suit, which includes a claim for damages, continues.