The unnamed offender is serving a five-year sentence for breaking into his ex-wife's NSW home and raping her in 2017.

While in custody, the Home Affairs department enforced a mandatory cancellation of the Indian man's regional sponsored migration scheme visa.

The department and the Administrative Appeals Tribunal later both declined to overturn the cancellation.

But the Federal Court this week ordered the AAT to review the case again after finding the victim's evidence about the effect of her ex-husband's deportation hadn't been properly taken into account.

While the impact on a victim usually supported the case to send an offender out of Australia, Justice Duncan Kerr was satisfied the relevant migration regulation required the victim be given "appropriate agency" in the visa process either way.

"The views of a victim are not controlling, but must be taken into account, whether they are adverse to or consistent with, the interests of the offender," Justice Kerr said on Monday.

The tribunal, which the judge said had otherwise given exemplary attention to its task, heard evidence that the former couple's seven-year-old son was suffering without his father.

"It's very hard for me at the moment ... he is not improving mentally," the victim said.

"He just keeps thinking this: 'why is my mum keeping me away from my dad?'

"And it's impacting him very badly."

She hoped her ex-husband, aged in his mid-30s, could assist her on weekends, telling the tribunal she was struggling.

"(The offender) did a mistake when he was drunk, and now after like this much time ... and giving him one chance, then it makes my life and my son's life a little bit easier, and he doesn't have to go through so much," she said.

Justice Kerr rejected the department's argument that the ex-wife's evidence rose no higher than expressing support for the offender to remain in Australia "so he could be more involved in his son's life".

It wasn't surprising a mother's focus was the wellbeing of her son, but that didn't mean the tribunal could effectively ignore "such humble evidence" about her own situation.

"She informed the tribunal that the impact of permitting (the offender) to remain in Australia would be of benefit to her. It would make her life a little bit easier," he said.

The decision doesn't mean her evidence will prevail when the AAT reconsiders the case at a later date.

The woman didn't get her way in 2018 when she requested the criminal prosecution be dropped.

The man had made significant admissions to police about breaking into his ex-wife's home while drunk and raping her.

He later pleaded guilty, with his sentencing judge finding he was contrite, remorseful, was unlikely to re-offend and had good prospects for rehabilitation.

The judge did note the man was convicted in 2016 for intimidation and contravening an apprehended domestic violence order after drunken rants.

He is currently eligible for parole.

Australian Associated Press