The Federal Court decision handed on Wednesday condemned acting Immigration Minister Alan Tudge's conduct as "disgraceful" and claimed it potentially exposed him to civil and criminal sanctions including contempt of court.

Justice Geoffrey Flick described the minister's behaviour as "not unprecedented" and warned Mr Tudge he was placing himself above the law.

The 34-year-old asylum seeker at the heart of the conflict, referred to as PDWL, applied for a protection visa in 2016.

More than three years later in December 2019 a delegate for the minister denied the visa on the grounds PDWL failed the character test after being convicted in March 2018 of a criminal offence.

On March 11 this year the Administrative Appeals Tribunal reversed the decision, on the basis that PDWL was not a risk to the Australian community.

The minister immediately appealed the decision and refused to release the refugee from the Yongah Hill Immigration Detention Centre in Western Australia - despite the tribunal decision. But he was released five days later following an earlier Federal Court ruling.

In his judgment, Justice Flick found the minister was not entitled to keep PDWL in detention merely because he had filed an appeal and no "real explanation" had been provided.

"He has intentionally and without lawful authority been responsible for depriving a person of his liberty," Justice Flick said.

"The Minister cannot place himself above the law. The Minister has acted unlawfully.

"His actions have unlawfully deprived a person of his liberty. His conduct exposes him to both civil and potentially criminal sanctions, not limited to a proceeding for contempt.

"In the absence of explanation, the Minister has engaged in conduct which can only be described as criminal."

A spokeswoman for the minister told AAP he "strongly rejects any suggestion of improper conduct in these proceedings" and he's considering options for an appeal.

Australian Associated Press