The Australian government will not challenge a Federal Court ruling that it has a duty of care to provide a safe and legal abortion for an African refugee raped on Nauru.

The ruling could become a landmark case, with human rights lawyers saying it shows the government has a duty of care for asylum seekers and refugees on Nauru and Manus Island - despite previously suggesting they were now the responsibility of those countries.

George Newhouse, principal solicitor with The National Justice Project - which ran the woman's legal case - said the case had broad implications.

"This important case shows that the government has a duty to take proper care of all detainees and refugees on Nauru and on Manus Island," he said.

On Tuesday, lawyers for Immigration Minister Peter Dutton wrote to lawyers for the woman, known only as S99, to say they would not appeal the Federal Court ruling handed down late on Friday.

In Friday night's ruling, Justice Mordecai​ Bromberg​ said that, despite the language the government used to describe the refugee, she "remains entitled to the protection of Australian law".

The young woman who, as Fairfax revealed last month, 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.

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

There she remains in limbo in a Port Moresby hotel room after her legal team issued emergency legal proceedings to prevent Australian authorities from arranging an abortion in PNG where, they say, her complex medical and mental health needs could not be assured.

She is now in her second trimester of pregnancy and, the court was told, her mental health is deteriorating rapidly.

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 last week set herself on fire on Nauru.

"I feel bad," she told her lawyers. "Can you please hurry up the court? My belly is growing bigger every day; I want the baby out."

In his ruling, Justice Bromberg said Australia must arrange for the woman to have a termination before May 15, either in Australia or another country (likely to be New Zealand or Singapore) with similar medical standards.

A spokesman for Mr Dutton said the government's "intent is to act in line with the court's orders".

In a statement, Mr Newhouse said she must now receive a safe and legal termination as soon as possible.

"She has entered the second trimester", he said. "It is imperative that the Turnbull government immediately brings her to Australia – or to another country where she can receive the highest standard of neurological and gynaecological care."