Refugee advocates have been criticising the Federal Government's handling of the woman for weeks, saying the Government has shown her little compassion.
They have welcomed the High Commissioner's call.
"Deeply traumatised and fragile."
That is how the spokesman for the United Nations' Office of the High Commissioner for Human Rights describes the alleged rape victim.
The 23-year-old asylum seeker is in her second trimester.
Her pregnancy is allegedly the result of an assault that happened while she was living in the community in Nauru.
Speaking in Geneva, Switzerland, the High Commissioner's spokesman Rupert Colville says she needs medical care fast.
"We call on Australia and Nauru to urgently provide a decent option for a woman called ... whose pseudonym is Abyan. It's the pseudonym of a Somali refugee woman. And she needs an option to obtain adequate mental and physical care and to terminate her pregnancy if she desires."
Mr Colville says the United Nations is disturbed by the increasing number of sexual-assault and rape allegations from asylum seekers sent to the small Pacific island.
And he says the United Nations is also disturbed by the failure to hold alleged perpetrators to account.
"(The Office of the High Commissioner for Human Rights) is concerned about reports that the Nauru police have failed to take action against the alleged perpetrators of violence against women, particularly when the victims have been asylum seekers and refugees. We are aware of a growing number of sexual-assault and rape allegations since Australia restarted its policy of transferring asylum seekers to Nauru for processing in 2012."
In Melbourne, the Human Rights Law Centre says the comments reflect the urgency of the woman called Abyan's situation.
Director of Legal Advocacy Daniel Webb said in a statement she is in an abhorrent position.
"Abyan came here seeking safety but has suffered great harm in our care. It's clear the only decent thing to do is bring her to Australia for the sensitive, professional medical treatment she needs. It's not about politics, it's a matter of basic human dignity."
After thousands of people petitioned Immigration Minister Peter Dutton, the Federal Government flew Abyan to Australia for a termination earlier this month.
But she was returned to Nauru days later, with the Department of Immigration saying she had changed her mind.
Abyan replied in a statement through her legal help that she never said she did not want a termination.
Her lawyers say she was not offered counselling.
In Melbourne, the Asylum Seeker Resource Centre's Pamela Curr has been in regular contact with her.
Ms Curr says the Government cannot simply dismiss the UN call for action.
"We really thank the Office of the High Commissioner for Human Rights for speaking out, because our Government is deaf to the rights of women."
SBS has sought comment from the Department of Immigration.
A report by the refugee advocacy group No Business in Abuse has accused the organisation operating the detention centres on Nauru and Manus Island of human-rights abuses.
It says Transfield Services has been complicit in 47 violations of international law, a claim Transfield rejects.
The report is based on publicly available information from independent third-party bodies and the results of parliamentary inquiries and legal cases.
Executive director Shen Narayanasamy says Transfield must share responsibility with the Government for what has happened at the centres.
"They're paid $1.4 million a day to run the detention centres. And as such, they're clearly responsible. Yes, the Government is also responsible, but that doesn't allow them to wash their hands of it."
Meanwhile, Federal Government efforts to strike a deal with the Philippines to permanently relocate asylum seekers now held in the two offshore detention camps have hit trouble.
Philippines president Benigno Aquino says now his country has no capacity to help Australia.
"If this proposed agreement is not one of a transitory nature, is not one of just being a transit point, but actually relocating these people here, we feel we are not in a capacity at this point in time to afford permanent residency to these people."
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