Churches Together in England (CTE) has six presidents, who jointly represent the whole membership - including the Catholic, Orthodox, Pentecostal, Anglican and Reformed churches.
Upon a presidency position becoming vacant, a group of Reformed churches and the Quakers nominated a woman who is in a same sex marriage for the role.
The appointment of Hannah Brock Womack to the Fourth Presidency position has not been well received by other denominations within the CTE.
As a result, Womack has been requested not to play any active role as a Churches Together president.
The member churches of CTE's enabling group stated: "For the sake of our ecumenical unity at present, we request that the Fourth Presidency Group show restraint by not exercising the office of their Presidential appointment."
Paul Parker, Recording Clerk for Quakers in Britain told Premier the dispute is an unnecessary distraction from the key issues Christians should be debating.
"The idea that it's her sexuality that means she's being rejected by other churches is just so disappointing," he said.
Parker says Quakers in Britain are "committed to continuing in conversation together" and Womack "recognises that churches have got a long way to go".
General Secretary of Churches Together in England, Revd Dr Paul Goodliff, told Premier taht theological divisions about gay relationships raise the deepest questions in today's churches.
"In the past it would have been other issues but this is the issue for our day for which our churches have to wrestle at the moment."
He went on to say that although the division is a cause of "great pain and sadness", he is hopeful the incident will not dissolve the movement as they "continue to pray and talk around these issues."
Hannah Brock Womack remains the fourth President but will not be able to take her place alongside the other CTE Presidents when they gather.
The fourth chair will be left empty as a symbol of the work still to be done to find unity.
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