The governors of the Anglican Centre in Rome announced Archbishop Bernard Ntahouri's resignation following an allegation of sexual misconduct.
Archbishop Bernard had also been the Archbishop of Canterbury's personal Representative to the Holy See.
In a statement the Centre's Governors said: "The Governors of the Anglican Centre in Rome have accepted the resignation of its Director Archbishop Bernard Ntahoturi following his suspension last week over an allegation of sexual misconduct.
"The Governors are now taking urgent steps to appoint an interim director, who will also act as the Archbishop of Canterbury's Representative to the Holy See."
Archbishop Bernard has held the role as Director since October 2017. Before he was ordained he was a civil servant who served as chief of staff to Burundi's President and served four years in prison following a military coup in 1987.
Previously he has held the position of Bishop of Matana and he also served as the Archbishop of Burundi.
The details of the allegation are not public knowledge.
The governors have said "anyone with a safeguarding concern or requiring support" to contact the Church of Englands safeguarding team.
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