Just opposite Borough tube stands Southwark's St George the Martyr Church, its eighteenth-century spire mirrored by the apex of The Shard that stands half a mile to the north. The saint from whom the church takes its name was killed in the year 303 for refusing to persecute Christians, and admitting he himself was one. Over a millennium later St George's Priest-in-Charge, Reverend Ray Andrews, has been fighting his own battle against discrimination.

Meeting me at the church door, the man known to his parishioners as "Father Ray" greets me with a warm handshake and an affectionate arm-squeeze. As the interview begins, we are interrupted by Andrews' mobile going off, blaring out the first few bars of Abba's "Dancing Queen". When I compliment him on a brilliant ring-tone he replies drily “it is very gay, though...".

Two years ago, when Andrews was approached to star in a documentary about an inner London clergyman, the filming process became a catalyst for him going public about his sexual preference for men, which he had hidden for decades. The documentary became Channel 4's cult hit Father Ray Comes Out.

The clergyman was originally reluctant to make the programme on the grounds that he did not wish to “hurt or alienate” anyone in his congregation, but his decision, he says, was vindicated by the reaction he received. He tells me that his revelation has only made his parish community “closer and warmer”.

Fuelled by this response, and encouraged by the fact that the church authorities didn't “find a way of getting rid of me or silencing me” - as he had feared - he is now uncompromising in expressing his disdain for homophobia.

I cannot help wondering why a man with such progressive views would choose to remain at the heart of a church whose leaders refuse to legitimise gay relationships. He explains that, for him, homosexuality and Christianity are not only compatible, but he thinks a belief in Jesus should preclude any kind of homophobia. "The Jesus I understand and experience defends the oppressed, tries to free the imprisoned, and feeds the hungry and the thirsty, and above all loves and includes. And so I can't claim to follow the teachings of that man, of God expressed in that way, and collude with the discrimination of homosexuality."

He says he has “no problem being in contradiction with scripture”, pointing out that scripture is not obeyed when it comes to the church marrying straight couples. “I have never married a heterosexual couple who have not either been living together beforehand, or been involved in a sexual relationship for quite a while. Never.”

This considered, how does he feel about the fact that current church law, soon to be underpinned by Maria Miller's "quadruple lock", will prevent him from blessing same-sex unions?

"If I am approached by two people who have encountered the gift of love and wish to affirm that before God, I would find that very hard to resist. I think if it comes to the point where I am directed to respond differently to two people of the same sex, to the way that I respond when heterosexual people marry, that will raise very serious questions about the future ”

Andrews is hopeful that it still might not come to this. As Maria Miller triumphantly points out in a blog for The Huffington Post, the decision regarding gay marriage is now out of the government's hands and rests with those responsible for canon law. Andrews feels that the church authorities will eventually have to change their stance, even if the motivation would be pragmatic rather than ethical.

He is keen to stress that the Church authorities' position on homosexuality, and the conception of a “judging, with-holding” God that it entails, does not reflect his ideas about his own faith. “For me, as I continue to grow older, I'm less convinced that when I hear the Church speak, I hear God speak.”

He is frustrated by the conservative image that the Church, with a capital 'c', is presenting in opposing gay marriage, and in November's synod vote against allowing women to become bishops, a decision which he says makes the institution look “rather ridiculous”. Does he think the Church is risking becoming irrelevant to contemporary life?

"We're doing a great job of that at the moment. We're losing credibility, we're not making sense. We should be leading the way. Where we see oppression, where we see injustice, where we see discrimination, we should be the ones who are leading the way.”

Why then, does he stay in an institution whose moral values seem to be so diametrically opposed to his own? He is conflicted, but says that ultimately he stays in the Church of England because he wants to “remain effective, making changes from within”.

And for Andrews, there remains a great deal to be done – he says he is still hearing the kind of homophobic rhetoric that frightened him in to self-denial for so much of his life. He expresses indignation at public figures like Baroness Warsi who suggested that speaking to children about homosexuality in schools might be dangerous. "The permission that people take to talk in this way is based on a huge lie, that homosexuality is a chosen behaviour, something we can teach and promote and undermine society with - rubbish, absolute rubbish!"

Ray tells me that many of his colleagues are in favour of gay marriage, and there are also a good number who have same-sex partners. However, they feel that being open with their relationships might put their careers in jeopardy, especially if they have ambitions to rise through the ranks of the Church. "There is a lot of pressure on senior clerics to conceal what might be a pro-gay position.”

Clearly drawing from his own experience, he expresses his will for those people to come forward and start breaking the silence. "It's the truth that sets you free. It might not be comfortable, it might not be easy, it involves risk, but it's the truth that sets you free.”