Dr Rowan Williams said he wanted to accommodate traditionalists
The Church of England's vote for women bishops will be an "obstacle" to reconciliation between Anglicans and Catholics, the Vatican has said.
The Church of England's General Synod voted in favour of consecrating women and against safeguards demanded by traditionalists opposed to the move.
A Church group will now draw up a code of practice to try to reassure critics.
But Roman Catholic leaders believe this goes against the will of Christ, who
chose only men as his apostles.
In a statement, Cardinal Walter Kasper, head of the Pontifical Council for the Promotion of Christian Unity, said: "For the future, this decision will have consequences for dialogue, which until now had borne much fruit.
"Such a decision is a break with apostolic tradition maintained in all of the Churches in the first millennium, and is therefore a further obstacle for reconciliation between the Catholic Church and the Church of England."
A draft of the code will be put before the General Synod in February.
It may not go far enough to satisfy some 1,300 clergy who had threatened to leave the Church if certain concessions, including allowing male "super-bishops" to cater for those opposing the change, were not met.
A final vote on the issue of women bishops is still several years away. Further revisions to the Church's code of practice could happen in 2010 and later a majority of dioceses in England would have to agree to having women as bishops.
That would lead to a further vote by the General Synod in 2011 or 2012.
Following six hours of debate on Monday, which saw one bishop in tears, the Synod rejected both the super-bishops proposal and the traditionalists' preferred option of new dioceses for objectors.
During the debate at the University of York, the pressure group Women and the Church said any such compromises would create second-class clergy and institutionalise division.
The Archbishop of Canterbury, Dr Rowan Williams, said he was deeply opposed to any system which would end up "structurally humiliating women who might be nominated to the episcopate".
Synod member and traditionalist Gerry O'Brien was hissed during the debate as he alluded to the American and Canadian Churches, from whom traditionalists have split in protest at the ordination of an openly gay bishop in 2003.
Mr O'Brien said: "We can force people out of the Church of England but I think the experience in America says you can't force people out of the Anglican Communion, because there are a lot of archbishops elsewhere in the world who will be more than ready to provide the support."
The first women priests in the Church of England were ordained in 1994.
The Scottish Episcopal Church has already cleared the way for ordaining women bishops, as have churches in the US, Canada, New Zealand and Australia.
But in May, the Vatican issued a decree which vowed to punish attempts in the Roman Catholic church to ordain women priests with automatic excommunication.