AN Afghan asylum seeker has won a reprieve from deportation after the federal government lost a legal challenge.

The 36-year-old man, from the Hazara ethnic minority, was granted a stay of deportation on November 24, one day before he was due to be deported to Afghanistan. Immigration Minister Chris Bowen unsuccessfully challenged the injunction in the Federal Court on Friday.

The Afghan, from the strife-torn Ghazni province, is the third failed asylum seeker Mr Bowen has been prevented from deporting because of pending cases before the full Federal Court. The others are another Hazara man and a Tamil asylum seeker from Sri Lanka.

The man arrived in Australia in 2010 claiming protection because he feared he would seriously risk being persecuted and possibly killed by the Taliban because he was a Shia Muslim and a Hazara.

Federal magistrate Philip Burchardt said the man would remain in Australia until February 1, after a case with near-identical facts was decided by the full Federal Court.

The case, involving another failed Hazara asylum seeker, centres on whether the court can review international treaty obligation assessments and the extent of the immigration minister's power to remove or allow failed asylum seekers to apply for a visa.

Magistrate Burchardt said the asylum seeker here had a "prima facie case" but that his decision did not imply it was probable the other case would win, only that it had a "sufficient likelihood of success".

He took into account the fact that the three Federal Court judges presiding over the other case had decided earlier in the week to add two more judges to the bench to continue the proceedings.

He also said that the asylum seekers in both cases were challenging different deficiencies in their negative international treaty obligation assessments.

Earlier this month, Debbie Mortimer, SC, called Mr Bowen's decision to deport the Hazara asylum seeker in the other case, referred to as SZQRB, "irrational" because it was made irrespective of whether earlier refugee assessments of the man were correct.

Mr Bowen's lawyer, Nick Wood, said there was no evidence that the immigration minister had decided against exercising his power to allow the man to apply for a visa as he had in SZQRB.