Dr Rowan Williams made the comments at an event for teenagers on how Christianity is viewed by non-religious people called "Help, my friends think I'm mad" at Lambeth palace.
According to the Daily Telegraph, Williams said the Church was wrestling with the issue gay marriage, in a tacit admission of homophobia in Anglicism.
"Same with same-sex marriage, where once more we're used to being alongside people who are gay; many of our friends may be – indeed we may be – wrestling with that issue ourselves, and the church is scratching its head and trying to work out where it is on all that, and what to think about it.
"What's frustrating is that we still have Christian people whose feelings about it are so strong, and sometimes so embarrassed and ashamed and disgusted, that that just sends out a message of unwelcome, of lack of understanding, of lack of patience.
"So whatever we think about it, we need, as a church, to be tackling what we feel about it."
The Archbishop’s intervention came shortly after the Church of England submitted its formal response to the government’s consultation on gay marriage, saying it could lead to it being forced out of its role of conducting weddings on behalf of the state.
The Church of England said several "major elements" of the proposals had not been thought through properly and were not legally "sound."
Several senior religious figures have spoken out against introducing gay marriage across all faiths, including the Chief Rabbi Jonathan Sacks and the Roman Catholic leader Archbishop of Westminster Vincent Nichols.
Responding to the Archbishop of Westminster in March Terry Sanderson, head of the National Secular Society, told The Huffington Post UK the law on gay marriage was "nothing to do with the Church" and "homophobia" was driving some religious leaders’ comments.
"I don't think there's any doubt that for all their double talk about it being about religious freedom homophobia does lie at the heart of it. If you see the sort of language the pope uses about gay people it's not just a kind of 'we stick by our biblical morals' it's a kind of 'we are repulsed by this'.
"I think it's very sinister really that these men are using these kind of language. The Catholic Church is shrinking in Britain but in other nations where there's already a culture of homophobia, it gives a kind of permission to be brutal towards gay people,” he said.
In April of Britain's most influential gay journalists launched an outspoken attack against the Church, saying it should beg for forgiveness for ruining the lives of gay people.
Matthew Todd, editor of Attitude Magazine and Stonewall journalist of the year, hit back at the Christian Church which he said "should be begging forgiveness from society because of the LGBT people whose lives it has diminished over the millennia."
During the event for Christian teenagers Dr Williams, who is set to step down as the Archbishop of Canterbury later in 2012, also said he was “very committed” to introducing female bishops.