The man, who is understood to have been granted refugee status, was allegedly removed without warning or legal representation.
Daniel Webb, the director of legal advocacy at the Human Rights Law Centre, said the man was not a client of his organisation, but did have a lawyer who was not informed of the removal.
"A decent and compassionate government which respects the rule of law doesn't choose to secretively deport people found to be refugees in the middle of the night without any transparency, due process or access to legal advice," said Mr Webb.
