The Archbishop of Wales says the church should offer gay people pastoral care and support.
Dr Barry Morgan's comments came in an address to the Church in Wales' governing body, meeting in Llandudno.
He expressed concern that gay people could feel unwelcome in churches in coming months, as the UK government proposals on gay marriage are debated.
He said the church could not ignore possible legislation, even though it would not mean gay church marriages.
The Archbishop described the issues surrounding gay relationships as facing "our church and the world" and that by raising the subject he was "entering a minefield".
He told his audience it was because "there are no easy simple answers to complicated ethical problems, nor is there a straightforward single Christian perspective on it, in spite of what some people may think.
"If the legislation to allow civil marriage is passed, I cannot see how we as a church, will be able to ignore the legality of the status of such partnerships and we ought not to want to do so.
"The question then as now is, will the church protect and support pastorally, faithful, stable, lifelong relationships of whatever kind in order to encourage human values such as love and fidelity and recognise the need in Christian people for some public religious support."
Gay marriage plans
The UK government launched a 12-week consultation on the issue of civil gay marriages in March, indicating that it wants gay couples to be legally allowed to make vows and declare they are married before the next general election, due in 2015.
It led to the leader of the Roman Catholic Church in Scotland, Cardinal Keith O'Brien, describing the proposals as "grotesque" plans that would "shame the United Kingdom in the eyes of the world" if implemented.
But the Archbishop of Wales warned: "Gays and lesbians claim they are still treated as second-class citizens, tolerated at best and vilified at worst.
"Very often homosexuality is talked about as if real people were not involved, and gays and lesbians complain of being talked about rather than talked to in church.
"The real question is, how do we hold together faithfulness to Scripture and tradition with the wider New Testament call to love our neighbour?"
Dr Morgan told the Church in Wales' governing body: "It is a discussion we need to have."