A gay man who has been living in the Australian city of Brisbane in a civil union will be deported next week to Pakistan after his application for a partnership visa was refused.

Ali Choudhry claims he is at risk of homophobic persecution if returned to Pakistan – a country where same-sex sexual activity is punishable with a prison sentence ranging from two years to life imprisonment.

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

Mr Choudhry and Dr Hynd were one of the first same-sex couples in Queensland to register their civil union on 12 March 2012, after the state introduced the measure.

Mr Choudhry does not understand why his request for a partnership visa has been refused.

“We applied for a partnership visa to try and keep me here, and keep us together,” he said to ABC News.

“For us, for whatever reason, it took about two years, and then even after all that time, it came back as a no.”

Dr Hynd remains pessimistic of what may happen.

“The worst case is, Ali will be deported next week on his birthday,” he said.

“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?”

A visa review was formally rejected by Immigration Minister Scott Morrison. A spokesman for Mr Morrison said that same-sex couples are assessed “no differently from heterosexual couples regarding immigration matters”.

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

Mr Choudhry has now lodged an appeal to the Migration Review Tribunal.