TONY EASTLEY: A gay man in Brisbane will be deported to Pakistan next week after his application for a partnership visa was refused, putting him at risk of being jailed in the country of his birth for being openly homosexual.

Ali Choudhry grew up in the United States and so has few contacts in Pakistan. As well, he cannot read or write the local language.

He's been in a relationship with Brisbane brain surgeon Dr Matthew Hynd for the past four years.

Nance Haxton reports.

NANCE HAXTON: Ali Choudhry and Dr Matthew Hynd were one of the first gay couples in Queensland to register their civil union on March the 12th, 2012. It was a significant day which they celebrated with family and friends after the ceremony.

But nearly two years later Mr Choudhry now faces deportation to Pakistan after his application for a visa recognising his relationship with Dr Hynd was refused. He says he cannot understand why theirs is not considered a legitimate long-term partnership.

ALI CHOUDHRY: We applied for a partnership visa to try and keep me here, and keep us together. And for us, for whatever reason, it took about two years, and then even after all that time, it came back as a no.

NANCE HAXTON: Mr Choudhry faces harassment and possible life imprisonment in Pakistan for being gay. His partner, Brisbane brain surgeon Dr Matthew Hynd, says they don't know what to do.

MATTHEW HYND: I mean, the worst case is, Ali will be deported next week on his birthday. You know, what do we do now? To go back to a country where, you know, there is life imprisonment for being gay.

And, I mean, he grew up in America, he's never lived in Pakistan. By country of birth, yes, but this is a country where he doesn't read the language - he can speak it - but how are you supposed to then get a job?

NANCE HAXTON: Mr Choudhry lost all his possessions in the Brisbane floods, but he has since set up a photography business in Brisbane. However he is now preparing for deportation on January the 8th.

ALI CHOUDHRY: Marriage equality and things like that are things that really do need to happen and happen soon, sooner than later. The response that I got on my initial day in there were, the fellow who was there that I should just get married. I mean, if I could, if I had that option I would do that.

NANCE HAXTON: He was notified two weeks ago that he must leave Australia after his visa review application to the Immigration Minister Scott Morrison was also rejected.

Mr Choudhry has now lodged an appeal to the Migration Review Tribunal, but may not find out if that application is accepted before his deportation.

The Immigration Minister was not available for interview for AM, but his spokesman said in a statement that same sex couples are assessed no differently from heterosexual couples regarding immigration matters.

He said while they cannot comment on individual cases for privacy reasons, all applicants must meet relevant criteria to be granted a visa and these extend beyond whether there is a genuine and ongoing relationship.

Dr Hynd says the ramifications of the visa rejection for both of them both are dire.

MATTHEW HYND: We have no idea what else we can do other than invite maybe the Immigration Minister into our bed and say, hey, this is two guys sleeping in the same bed; if you do not believe that, you know, we're in a relationship, then I just don't know.

TONY EASTLEY: Dr Matthew Hynd ending Nance Haxton's report.