FOI documents have revealed Australian Government claims that a Somali refugee raped on Nauru had changed her mind about an abortion were incorrect.

Somali woman Abyan’s case gained national prominence earlier this year after medical staff at Nauru’s Australian Government-run detention facility advised there were health risks if she did not receive an abortion, and requested she be transferred to Australia as soon as possible.

The documents show that on arrival at the Villawood detention facility in NSW, Abyan indicated she was not “mentally well enough” to undergo the procedure on arrival, but that she had not changed her mind and was aware she had up to 20 weeks into the pregnancy to make her decision. However, after just five days in Australia, she was returned to Nauru.

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Human rights lawyer Kellie Tranter who made the FOI requests for the documents said they clearly showed senior public servants, if not the Minister, knew Abyan had not refused a termination.

"The reason that those documents are so interesting and disturbing at the same time is that Minister Dutton’s position is somewhat skewered because if he was misinformed, one wonders whether he can trust his own department to give him accurate advice, if he wasn’t misinformed the Minister has seriously mislead the public and the parliament when he said Abyan decided not to proceed with the termination," Ms Tranter told SBS World News.

Immigration Minister Peter Dutton said at the time that Abyan had changed her mind about the abortion and that she was to be returned to Nauru.

"The woman has decided not to proceed with the termination," Mr Dutton said in a statement on October 17. This was also supported by comments from Prime Minister Malcolm Turnbull the same day.

Mr Dutton accused refugee advocates who disputed this version of events of lying.

"Comments from some advocates ... are a fabrication, while others appear to be using this woman's circumstance to their own political agenda," the statement read.

It is unclear from the documents why Abyan was removed when she had not rejected an abortion, as claimed by the Minister, however a note in the FOI documents from Australian Border Force warned: "There is a risk that once in Australia, [Abyan] will seek to join legal action which would prevent her return."

Ms Tranter said the fear expressed in the comment that Abyan would use the abortion to try and stay in Australia, was disturbing, given the matter involved a rape victim.

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"In Abyan’s case she had clearly been raped and the initial concern about her health had not been raised by her lawyers or by her, it was raised by the International Health and Medical Services on Nauru," she said.

"So there was no racket in her case, there was no attempt by her to engineer her way into the country so she could somehow get a migration outcome. The fact that her case was shrouded with such suspicion says a lot about the mindset of the people working in the department itself."

The documents also reveal that Australian officials were anxious to find an “on-island solution” and were at first against Abyan being brought to Australia, except as a last resort.

Ms Tranter called for a royal commission into the Immigration Department’s handling of refugees and asylum seekers.

"I think any department that operates in such secrecy, this culture develops impunity; so I absolutely believe an independent and or royal commission is warranted because we need to look at the function, structure and operations of this department," she said.

Abyan was later returned to Australia a number of weeks after her initial trip to receive medical assistance in Brisbane.

Comment has been sought from the Immigration Minister, Peter Dutton.