Immigration Minister Peter Dutton owes a young African refugee raped on Nauru a duty of care, and must not force her to terminate her pregnancy in Papua New Guinea where it is neither safe nor legal, the Federal Court ruled on Friday.

But uncertainty still surrounds the woman's fate, with Mr Dutton and his department under no obligation to bring her to Australia for a safe and legal abortion - only to ensure she receives one.

The young woman, who was semi-conscious after suffering a suspected epileptic seizure when she was attacked on Nauru, had begged authorities to let her come to Australia to terminate the pregnancy she does not want.

Instead, Australia sent her to Papua New Guinea, where the criminal code states abortion is illegal.

Since then the woman, known only as S99, has spent a month in limbo in a Port Moresby hotel room, as first the High Court, and then the Federal Court, considered her fate.

Her barrister, Ron Merkel, told the court the woman had told her legal team on Thursday she felt she was "going crazy" and said she might hurt herself "like Hodan" - a reference to the young Somali woman who this week set herself on fire on Nauru.

Handing down his findings late on Friday, Justice Mordecai Bromberg told the court the woman must be considered under the protection of Australian law, despite the fact she lives in Nauru.

"She has no independent means," Justice Bromberg told the court. "She has been and remains dependent on the Minister for food, shelter, security and healthcare."

Justice Bromberg said Australia, by extension, had a duty of care to provide the woman with a safe and lawful abortion.

Lawyers for the government had denied Australia owed the woman a legal duty of care.

David Nockels, assistant secretary of Australian Border Force's detention services division, told the court last week sending the woman to Australia would have breached immigration policy.

"From a policy perspective in terms of bringing people back to Australia if there are other alternatives ... we would pursue that," he said.

"That's why we have Nauru and Manus ... that's the policy perspective."

The court had been told the woman suffers from violent and regular seizures for which she receives medical care, and which would require specialist medical attention if she was sedated for a termination.

She also has severe mental health issues, special medical needs from a medical procedure she was subjected to as a young girl, and has tried to harm herself following her rape.

The court was last week told that Australia has referred at least two refugee women (including the woman known only as S99) for pregnancy terminations at Pacific International Hospital (PIH) in Port Moresby.

Abortion is illegal in Papua New Guinea, according to its criminal code, which states a woman who attempts to "procure her own miscarriage" faces a maximum seven years' imprisonment. Last year a PNG couple were jailed for five years for causing the death of their unborn child.

Justice Bromberg said it was unreasonable to consider an abortion procured in Papua New Guinea either a safe, or a legal, procedure.

The woman's barrister Ron Merkel told the Federal Court that Australia sending the woman to PNG for an abortion was tantamount to it "procuring illegal conduct".

Justice Bromberg forbade Australia from procuring an abortion for the woman in Papua New Guinea, but did not require her to be brought to Australia.

It's expected a third country will now need to be found for her termination.