A Federal Court judge has blasted a Commonwealth tribunal after it concluded homosexuality is fixed at birth and cannot change over time, branding the decision "illogical" and based on "assumptions, pre-conceptions or pre-judgments" about human sexuality.

Justice Jayne Jagot said the Administrative Appeals Tribunal (AAT) failed to "properly satisfy itself about critical facts" when it affirmed an immigration department decision refusing a Lebanese woman a temporary partner visa on the basis she was not in a genuine relationship with her husband.

The woman came to Australia in December 2009 on a student visa and remained in the country illegally between December 2013 and October 2014 before marrying her husband, a Lebanese man in Australia on a protection visa, and applying for a temporary partner visa.

According to the AAT, the woman's husband had been granted a protection visa on the basis of his homosexuality and feared persecution in Lebanon.

The tribunal wrote to the woman in January last year and said it was "difficult to see how the sponsor can have a commitment to his marriage to you when he has not told you about his claimed homosexuality".