Australia ignored urgent pleas from its own medical experts to bring a refugee raped on Nauru to Australia for an abortion.

The Federal Court is considering the case of a young African woman, known only by the pseudonym S99, who was in the midst of a violent epilepsy seizure and barely conscious when she was raped on Nauru. Abortion is illegal in the tiny island nation.

The woman told the court on Thursday that she had realised she had been raped only when she discovered blood and "male discharge" on her person.

As Fairfax Media revealed last month, the woman's legal battles began when she begged Australian officials on Nauru to let her come here to terminate the pregnancy she does not want. Instead, Australia sent her to Port Moresby for an abortion.

Abortion is also 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.

On Thursday, it was revealed the Department of Immigration and Border Protection ignored repeated requests from IHMS, the company it contracts to provide health services on Nauru and Manus Island, to bring the woman to Australia for an urgent termination.

In a letter to the department, IHMS warned that the woman faced long-term health and psychological consequences if she was forced to endure a pregnancy she did not want.

It also said the woman's epilepsy and another health condition, which Fairfax is prevented from disclosing due to a non-publication order imposed on Thursday, posed grave risks to her physical and mental health.

"The mental health risks are greater the longer the pregnancy progresses against her will," the report said.

The report said the woman was at risk of "significant mental health issues" both in pregnancy and afterwards, and that if her pregnancy was not terminated, she risked developing post-natal depression and not engaging properly with her baby.

But in a letter sent on Tuesday, David Nockels​, the first assistant secretary of the detention services division of the Australian Border Force, rejected that advice. He remained of the view the Pacific International Hospital in PNG was an appropriate place for the woman to undergo her abortion.

Appearing via videolink from Port Moresby, where she remains in limbo after an emergency court order was imposed preventing an abortion being carried out until the current case is resolved, the woman told the court through an interpreter that she had not known she was being sent to PNG.

She said she signed a document she did not understand, or read, only after being told she would be taken to a third country for mental health treatment, dental treatment (for teeth broken during an earlier seizure), treatment for her seizures and to have her pregnancy terminated: "to get my health back".

Asked whether she knew where she was being taken, she said: "no".

The case continues on Friday.