George Newhouse, the man's solicitor, argued the risk of harm to him if he was sent back to his homeland had not been assessed according to changes to the Migration Act, which came into effect in March.

"The considerations are broader under the new test than under the old rules, before the pre-March 2012 changes," Mr Newhouse said.

The injunction is until 72 hours after the court delivers its judgment in that case.

Mr Newhouse said the Tamil man still had an arguable case in relation to Australia's complementary protection obligations.

He agreed that his argument for the application had not changed, but said he was "not at liberty to discuss" why the decision was overturned.

The Tamil man, in his 40s, lost his application for an injunction at the Federal Court on Tuesday. An ambulance was called to the detention centre early today.

A Department of Immigration spokeswoman confirmed that he had engaged in an act of self-harm, and said the incident did not affect the outcome of his protection claim.

She said paramedics treated him on site for minor injuries, but he was not taken to hospital, and had ongoing access to mental health support, including psychologists, mental health nurses and counsellors.

The Tamil man arrived in Australia two years ago, and had said his brother was a separatist Tamil Tiger fighter in Sri Lanka. Last week, he was given his deportation orders after he had exhausted legal appeals for protection, and refused to sign them.

The spokeswoman would not comment on the details of his scheduled deportation or today's appeal.

Tamil community advocate Aran Mylvaganam said a security guard at Maribyrnong Detention Centre, where the man is being held, had told him the news of the injunction and moved him to a private room.

For the past two days Mr Mylvaganam said the man had called him hourly to ask him if he can stop his deportation.

"One of the things that he's told me is he'd be killed if he's sent back to Sri Lanka so hearing this news that he's not going to be deported, he'll be very happy."

Earlier today, refugee advocates blocked the exit of the detention centre in a bid to prevent his deportation.

About 30 people linked arms in a line outside the Hampstead Road exit of the centre.

Refugee Advocacy Collective spokesman Benjamin Solah said many of the protesters had been at the centre since 7am, chanting "We shall not be moved" and "Free the refugees".

The case follows Australia's first deportation of a Tamil asylum seeker, Dayan Anthony, in July since the three-decade Sri Lankan civil war ended, despite a last-minute appeal to the United Nations.

Mr Newhouse said lawyers were running a similar case about Australia's complementary protection obligations on behalf of another Tamil asylum seeker. That case will be heard by the full Federal Court in mid-November.