The man has been sent back to Sri Lanka despite official Australian advice warning people against travelling to the northern city of Jaffna where he lived.
The UN human rights commissioner in Geneva had sent the urgent request to the Australian embassy in Thailand early yesterday morning in the hope of getting the man off a plane in Bangkok while on the way back to Colombo.
But the man, who The Age has chosen not to name at his familyâ€™s request, was taken back to Sri Lanka, where supporters have been unable to contact him.
The Immigration Department said the UN request came while the man was on the plane from Bangkok, and did not raise any information not already considered in rejecting his refugee claim.
â€œIn this instance, timing and practicalities clearly precluded such consideration,â€™â€™ a spokesman said.
Sri Lankan media have named the man, including his photograph, and published an apparent arrest warrant in his name, raising fears he will be the target of reprisals. He was deported from Melbourne on Wednesday after exhausting all appeals for a refugee visa, including a request for a review by Immigration Minister Chris Bowen.
But his supporters lodged a complaint with the UN Committee on Torture the day he was deported, leading the UN to ask that Australia â€œrefrainâ€™â€™ from returning the man to Sri Lanka while his complaint was under consideration.
A human rights lawyer, Phil Lynch, said it appeared to be the first time Australia had defied a UN request of this type, which are issued only rarely.
â€œIt is the international equivalent of an urgent legal injunction,â€™â€™ he said.
Despite the UN bid, recriminations are rife among refugee advocates wondering why the man had not earlier been made a party to a High Court challenge that would have effectively blocked his deportation.
About 150 other asylum seekers who have failed in their bid for refugee status are party to
the case into the discretion of the minister to review visa claims.
Immigration authorities have promised not to deport anyone waiting for the courtâ€™s decision, expected before October.
Victorian Legal Aid had been advising the man, but his lawyer declined to comment yesterday, citing legal privilege.
An apparently faulty fax machine at the Maribyrnong detention centre, where the man had been held before his deportation, had stopped him sending a letter authorising his lawyers to act on Monday and Tuesday.
Meanwhile authorities have intercepted a boat carrying a suspected 52 asylum seekers off the West Australian coast, who will be taken to Christmas Island, where they will undergo checks.
SMH With AAP