Dr Williams said the Church was "anxious and tormented"
The Archbishop of Canterbury has said Jesus would feel the pain on both sides of the divide in the Church of England over women bishops and gay priests.
Rowan Williams made his comments during a sermon at a communion service at York Minster ahead of a crucial vote by the Church's ruling body.
On Monday, the General Synod will decide how far the Church should accommodate opponents of women bishops.
More than 1,000 clergy have threatened to leave the Church over the issue.
They say they will go unless adequate safeguards are put in place to ensure they can receive pastoral oversight from a male bishop.
The controversy comes shortly after the creation of a worldwide movement of Anglicans who oppose the liberalisation of Church teaching on issues such as homosexuality.
Dr Williams said: "In the middle of our discussions at Synod, where would Jesus be?
"Jesus is going to be with those who feel the waterlessness of their position, with those traditionalists feeling the Church is slipping away from them, the landmarks have shifted....
"He will be with those in very different parts of the landscape who feel that things are closing in, that their position is under threat and their liberties are being taken away by those anxious and eager to enforce new ideologies in the name of Christ.
"He will be with those who feel that their liberty of questioning is under threat, he will be with gay clergy who wonder what their future is in a Church so anxious and tormented about this issue."
Any decision on woman bishops will have to be approved by parliament.
Christina Rees is a campaigner for women bishops
Conservative MP, Robert Key, who sits on the Synod, said MPs could vote against any measure they thought was unfair.
"MPs don't see this as a theological squabble in the Church of England. They see it as something much broader," he said.
The Church of England has refused to confirm newspaper reports that senior bishops have had talks with Vatican officials over divisions in the Anglican Communion ahead of the Lambeth Conference later this month.
The Sunday Telegraph reported that Church of England bishops met senior advisers of Pope Benedict XVI to discuss the issue of gay priests and women bishops.
A number of bishops within the worldwide Communion have declined invitations to Lambeth - which takes place every 10 years - in protest at the presence of pro-gay clergy.
Meanwhile, a proposal to assist the opening up of hundreds of parish churches to tourists has been approved by the General Synod during its gathering at York University.
Members backed calls for the creation of a tourism group in each of the 44 dioceses to boost interest in church buildings.
The meeting was also due to debate whether fees charged for weddings and funerals should be raised.
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