A baby born to an asylum seeker in Brisbane is not entitled to apply for a protection visa, a Federal Circuit Court judge has ruled.

Ferouz Myuddin, now 11 months old, was born prematurely in Brisbane's Mater Hospital at South Brisbane in November 2013 after his mother was transferred from the detention centre on Nauru due to concerns about her pregnancy.

Immigration Minister Scott Morrison had denied him a protection visa, saying he was an unauthorised maritime arrival.

Lawyers for the baby challenged the ruling, but that was dismissed by Justice Michael Jarrett of the Federal Circuit Court in Brisbane on Wednesday afternoon.

Ferouz and his family now live in detention in Darwin, but are originally from Myanmar.

He was one of about 100 babies born on Australian soil to asylum seeker parents who arrived via boat represented by Maurice Blackburn Lawyers.

Mr Morrison said in a statement this afternoon the "Government welcomed the outcome of the case in the Federal Circuit Court".

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"It has always been the intention of successive governments that children born to illegal maritime arrivals, are taken to have the same status as their parents," Mr Morrison said.

"The Government has legislation before the Parliament that reinforces the outcome in this case and ensures that these cases continue to be treated consistently with the Government's policy."

'Let these Aussie kids stay'

Maurice Blackburn senior associate Murray Watt said he had spoken to the family and they would file an urgent appeal against the decision to the full court of the Federal Court of Australia.

"While we respect the decision of the court, Ferouz's family are obviously very distressed by [Wednesday's] verdict," Mr Watt said.

"All they have continued to seek for Ferouz is a fair go: Ferouz was born in Brisbane and has a Queensland birth certificate, and we remain firmly of the view that on that basis he should have the right to seek protection in Australia."

He said the fate of Ferouz and 100 other babies like him in detention rested on the appeal and in the hands of Federal MP Clive Palmer.

"Amendments to the Migration Act, which are currently before Federal Parliament, would result in the transfer of all the babies to Nauru, despite being born on Australian soil," Mr Watt said.

"It is now more critical than ever that all Australian members of Parliament - particularly those with the balance of power - vote against these amendments and let these Aussie kids stay."

He also said the decision did not have any bearing on Ferouz's Australian citizenship application.

"Around the same time as we applied for his protection visa in December last year... we separately applied for Ferouz to have Australian citizenship," Mr Watt said.

"The basis of his application is that under the Australian Citizenship Act, if a child is born in Australia, and is considered in legal term as 'stateless', which means that they're not entitled to the citizenship of another country, then that child is entitled to apply for Australian citizenship."

Mr Watt said Ferouz and his family were originally from an ethnic minority in Myanmar, which is also known as Burma.

"The United Nations has recognised that that ethnic minority was one of the most persecuted groups in the world," he said.

Mr Watt said the Myanmar government passed laws many years ago that denied citizenship to that particular minority.

"His entire family are actually not entitled to citizenship in the country that they originally came from and they are not entitled to citizenship from any other country, so they are stateless," he said.

"We argue that that means that Ferouz, having been born here, and being stateless, is entitled to apply for Australian citizenship.

"We have not received a response from the department to that application despite it being lodged getting on towards 12 months ago."

Ferouz and his family remain 'stateless'

Speaking outside court, the chair of the Australian Churches Refugee Taskforce, Dr Peter Catt, said even if given refugee status and released, baby Ferouz and his family would "remain stateless".

"Nauru has said it won't resettle anyone longer than five years, so we consign baby Ferouz to an early childhood of detention and deprivation, and then what happens when he comes of school age?" he said.

He said the taskforce was "greatly saddened" by the court's decision.

"We are now extremely fearful for the fate of 100 babies and their families, whose future lies in this decision," Dr Catt said.

"They could be sent offshore in 24 hours' time, to the hellish conditions we know exist on Nauru."

He said Mr Morrison wanted to "clear a desolate path so he can send this Brisbane-born baby and his family back to the detention camp on Nauru".

"This is legal gymnastics - it is deeply disturbing that the Minister for Immigration has so desperately sought to deny baby Ferouz a fair chance at having his claim for protection and possible Australian citizenship heard," he said.

"How can we rationally call babies born in Australia 'boat people'?"

Misha Coleman, executive officer of the taskforce, said she first met the family in the Brisbane detention centre.

"Mum Latifa had just been separated by the Australian Government from her newborn baby, Ferouz," she said.

"Ferouz's dad had been on the run since the Burmese army killed his own father when he was seven years old.

"How much more do we need to put this family through?"

Decision to affect fate of all asylum seeker babies: lawyer

Mr Watt said on Tuesday the fate of 100 asylum seeker children rested on the outcome of Wednesday's case.

"Ferouz has spent his entire life behind razor wire with the Federal Government having spent the past year putting up legal hurdle after legal hurdle to deny him protection in Australia," he said.

"Ferouz was denied a protection visa by the Government on the basis that they said he came by boat and was therefore an "unauthorised maritime arrival".

"This is a ludicrous decision given he was born here in Brisbane's Mater Hospital and he even has a Queensland birth certificate."

Mr Watt had said they were challenging the Department of Immigration's decision that a boy born in an Australian hospital came here by sea.

"If we're successful, then that means that the department needs to consider his application for a protection visa on its merits," he said.