The asylum seekers – who cannot be named – emailed refugee lawyer David Manne from Christmas Island on Wednesday seeking his help to apply for refugee protection.

The email came after 31 Tamil asylum seekers were flown from Christmas Island to Sri Lanka after they were determined to be not genuine refugees. Daniel Webb, from the Human Rights Law Centre, said that such people were typically interviewed without legal advice.

Lawyers applied to the Federal Circuit Court for access to the two people and 12 others who they also believed wanted legal assistance. After negotiating with Mr O'Connor's lawyers for a number of hours, they agreed on Thursday that the manager of Christmas Island's detention centre would "make available facilities at certain times and circumstances" for the two asylum seekers. They also agreed to provide two business days' notice before removing them from Australia.

Lawyers are still discussing what will happen to the other 12 asylum seekers.

"It's been necessary to go to court in order for the government to allow these people to get legal help in relation to their basic rights so that they know where they stand and are able to make any claims for protection as refugees in Australia without being expelled to Sri Lanka," Mr Manne said.

He said there were still concerns for others in detention without access to legal representation.

"If people don't know their rights and aren't able to present their claims and there's a miscarriage of justice... we could be sending people back to the real risk of torture or death."

Under current law, the government must give people in immigration detention "all reasonable facilities... for obtaining legal advice or taking legal proceedings in relation to his or her immigration detention" at their request.

Nick Wood, for the Immigration Minister, said the government was required only to organise free legal assistance for asylum seekers when they asked a Commonwealth official for it.

Justice Grant Riethmuller questioned whether asylum seekers would understand that legal assistance would be free. "They should be aware of that in order to then make an informed decision of whether or not to request [legal assistance]," he said.

The judge also said that Australians in prison for criminal offences were by contrast given weekly access to legal aid lawyers.

Mr O'Connor declined to comment on the case but said that people whose claims were not covered by the Refugee Convention would "be returned to their homeland wherever possible".

The case was adjourned until 3 June.

Meanwhile, Mr O'Connor will challenge a ruling that his predecessor, Chris Bowen, illegally ordered a man's removal to Afghanistan in the High Court.

The man, who cannot be named, arrived in 2010, claiming that the Taliban would kill him if he returned. He was scheduled to be flown to Afghanistan last September, having failed his refugee assessments.

The case is expected to determine the extent of the minister's personal legal powers to grant failed asylum seekers a visa if it is in the public interest.

Mr Bowen, then the immigration minister, said he would not consider using the powers, even if he was wrong and even if the assessments of the man were factually or legally wrong.

In March, the court unanimously declared Mr Bowen's decision invalid and the Hazara man's previous refugee assessment unlawful as he had been denied procedural fairness. They prevented the minister from removing him from Australia ''until the claims for protection ... have been assessed according to law''.