A Somali refugee who alleged she was raped in Nauru will be flown to Australia for a second time to potentially have an abortion, the Australian government has said.

The announcement comes a day after the UN's human rights agency demanded she get another opportunity to have her 15-week pregnancy terminated.

The case of the 23-year-old woman, known by the pseudonym Abyan, has amplified criticism of the Australian government's policy of refusing to allow asylum seekers who arrive by boat to settle in Australia under any circumstances.

Asylum seekers who attempt to reach Australian shores are transferred to Australia-run immigration detention camps in the impoverished Pacific island nations of Nauru and Papua New Guinea.

Australia flew Abyan 2,500 miles (4,000 kilometres) to Sydney for an abortion on October 11, but she returned five days later still pregnant. The government said she had changed her mind.

Immigration Minister Peter Dutton said he was concerned that 240 asylum seekers who flew to Australia for medical treatment then got court injunctions preventing their return to Nauru.

Mr Dutton said that Abyan would return to Australia to consult a doctor and receive mental health support, but would not say when.

He said the move had not been prompted by the UN criticism.