The Archbishop of the Church of Uganda walked out of the Primates Gathering in Canterbury on Tuesday amid accusations he was being "manipulated".
Archbishop Stanley Ntagali moved a resolution to ask the US Episcopal Church and the Anglican Church of Canada to leave the meeting because of their liberal stance.
He said he had no other option but to leave the meeting after this request was rejected.
"They would not agree to this request nor did it appear that the Archbishop of Canterbury and his facilitators would ensure that this matter be substantively addressed in a timely manner," he said.
The African Churches have been at odds with the more liberal churches in North America over their stance on homosexuality.
The Primates meeting was designed to stop a break up in the Anglican Communion over the issue.
Archbishop Stanley said: "Sadly, after two long days of discussions, I was concerned that the process set up for this meeting would not permit us to address the unfinished business from the 2007 Primates Meeting in Dar es Salaam.
"In accordance with the resolution of our Provincial Assembly, it was, therefore, necessary for me to withdraw from the meeting, which I did at the end of the second day.
"It seemed that I was being manipulated into participating in a long meeting with the Episcopal Church USA and the Anglican Church of Canada without the necessary discipline being upheld. My conscience is at peace."
He stressed that he was not leaving the Anglican Communion but suggested it did not include the American churches: "Together with our fellow GAFCON [Africa] Provinces and others in the Global South, we are the Anglican Communion; the future is bright.
"The door is open for all those who seek communion on the basis of a common confession of our historic, Biblical faith.
"I have never been more happy and proud to be part of the Church of Uganda."
The meeting continued without him and is expected to finish tomorrow.
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