The woman, 23, was sent back without the abortion having taken place, Australian media reports say.
The government made the decision after concluding the woman had changed her mind, they said.
But advocates assisting the woman say she was seeking counselling over the issue first.
Under Australia's asylum policy, any undocumented migrants trying to reach the country by boat are intercepted and held in centres on Nauru and Manus Island, Papua New Guinea.
The Australian government has not officially commented on the reports.
On Twitter, Australian Greens senator Sarah Hanson-Young said it was "hard to fathom a more brutal way of treating a young woman traumatised by rape and now pregnant".
On Thursday, Immigration Minister Peter Dutton said in a radio interview that refugees and asylum seekers on Nauru were asking for medical care in Australia in order to try and have their refugee claims processed on the mainland.
He described the behaviour as a "racket".
Abortion is illegal in Nauru, except where the mother's life is at risk. Rape is not considered a justifiable reason to seek a termination.
Earlier this week, the Nauru government said that another Somali refugee who alleged she was raped could face charges for making a false complaint.
The authorities said there was insufficient evidence to support the woman's claim she was raped by two Nauruan men.
The Australian government says its asylum policy deters people-traffickers but there has been been criticism of the conditions at the camps.
In September, a report by the senate committee found conditions on Nauru were not "appropriate or safe". It said allegations of rape and abuse should be investigated.
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Australia's controversial asylum policy
A Somali woman who was allegedly raped on Nauru and brought to Australia for an abortion has reportedly been flown back to the island.