The Archbishop made his comments the day after Gene Robinson was consecrated as the first openly gay bishop in a ceremony in New Hampshire.
''The divisions that are arising are a matter of deep regret, they will be all too visible in the fact that it will not be possible for Gene Robinson's ministry as a bishop to be accepted in every province in the communion'', said Dr Williams.
The Archbishop went on to say that it was important for the Anglican church to deal head on with issues arising from the controversial appointment.
''It is clear that those who have consecrated Gene Robinson have acted in good faith, but the effects of this upon the ministry and witness of the overwhelming majority of Anglicans particularly in the northwestern world have to be confronted with honesty''.
Gene Robinson, 56, a divorced father of two, has become the first bishop of a major Christian denomination to openly live with a same-sex partner.
Despite warnings from the church of a permanent split within the Anglican community, Robinson has refused to step down and repeatedly predicted that his consecration will open the doors for other homosexual bishops.
"There are extraordinarily gifted gay and lesbian people in serious positions of leadership throughout our church. They will be nominated as well. My stepping aside would not stop this one bit," Robinson said.
So vehement is some of the opposition to the idea of an open, sexually active gay bishop that Robinson had been given police protection after receiving numerous death threats.
At Robinson's ceremony, the Bishop of New York, David Bena spoke for 38 opposing Bishops in the Episcopal Church and the Anglican church of Canada.
Bena said that most bishops in the Anglican church worldwide would not recognise Robinson as a bishop.
The Anglican Bishop of Sydney, Peter Jensen added to the controversy saying that he was saddened at the appointment ''because the word of God teaches us what the standards are for Christian behaviour in leaders and Canon Robinson does not fulfil those requirements.
Some within the church are predicting that the backlash against Robinson has only just begun, and predict this to be the worst split in the Episcopal church since it's foundation in 1789.