The Nauru government has blocked the transfer of a critically ill refugee to Australia for healthcare, despite a court order, because a senior official was “not convinced” she needed it, the federal court has heard.

The move comes as a refugee blinded in the 2014 attack on the Manus Island centre has finally been transferred to Australia, more than a year after doctors made urgent recommendations.

On Monday the Australian federal court ordered the Australian home affairs minister transfer the critically ill woman on Nauru, who suffers from a number of mental illnesses including post-traumatic stress and depression, to Australia within 48 hours, accompanied by her brother.

However, according to the ABC, the Nauruan secretary of multicultural affairs refused to approve an air ambulance transfer, because she was “just not convinced” it was a medical emergency.

At a new hearing on Wednesday, lawyers for the refugee told the court the refusal left the Australian minister and department in breach of the Monday orders, despite it being because of the Nauru official’s actions.

The ABC reported the minister’s lawyer, Dejan Lukic, told the court the Nauruan government was sensitive to perceptions people were not treated well or did not receive adequate healthcare in its country.

Nauru is currently hosting the Pacific Islands Forum, and has been particularly sensitive to media focus on refugees – dismantling the much-criticised tent accomodation in the family compound prior to the forum and only allowing journalists to visit refugees with a government minder.

Justice Debbie Mortimer said there was no evidence that “day-to-day” care on Nauru was insufficient. However she described this as an “extreme” case, and said there was evidence about the medical care available for extreme cases.

“I don’t want this woman prevented any longer than necessary from leaving Nauru,” Mortimer said. “It’s a very serious matter for the home affairs minister to be in breach of orders.”

Mortimer amended Monday’s orders, giving the department 60 hours to comply. The court was told there were arrangements in place to have the woman flown to a New South Wales hospital on a commercial flight.

Monday’s orders included access to a Farsi interpreter and an undertaking that the department give the refugee’s lawyers at least two days notice of any move to transfer her or her brother out of Australia.

Lawyers for the refugee expressed concern the Nauruan government would attempt to block the transfer again but Lukic said the woman’s temporary settlement visa in Nauru meant there was no obstacle to her taking a commercial flight, if the receiving country approved the visit.

The Nauruan government has been contacted for comment.

In a separate federal court order, an Iraqi refugee who was left blind after being attacked by guards and rioters inside the Manus Island detention centre in 2014 has been finally moved to Australia, more than a year after doctors said he needed to be urgently transferred for hospital treatment.

Guardian Australia reported on Mohammed Hamza Hussein’s case in August. He lost all sight in his right eye when he was beaten with a post during the 2014 attack on the Manus detention centre but, in the years since, has also begun to go blind in his other eye.

Ophthalmologists have repeatedly told the Australian government he requires urgent intervention – including treatments not available on Manus Island – in order to save his sight.

“I’m the father of four girls,” Hussein, 46, a former Iraqi policeman, told Guardian Australia through an interpreter “but I’ve been locked up here for five years … I want to be able to see my family again.”

Hussein attempted suicide and survived only after friends intervened. Serious concerns remain for his deteriorating mental health.

Following significant public and legal interest in his case, Hussein was flown to Port Moresby, despite the hospital there saying it could not adequately treat him. In a hearing last week, the federal court in Melbourne ordered that Hussein be brought to Australia for hospital treatment.

He is currently in Brisbane.

There have been numerous instances of critically ill refugees having to take their cases to court to get a medical transfer to Australia. The Australian government has fought – and lost – several cases involving children.

A coalition of dozens of human rights groups and charities, including World Vision, has given the government a deadline to get all children and their families off Nauru by Universal Children’s Day on 20 November.

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