Richard and Caroline Crocker are to cease in their roles as General Secretary and Director of Communications in the Evangelical Fellowship in the Anglican Communion (EFAC).
The EFAC Council and Executive said it was "with regret" that the decision had been reached not to renew the Crockers' positions beyond the end of July.
In a statement, Bishop Stephen Hale, Chair of the Executive, and Bishop Keith Sinclair, Chair of the Trustees, said there were "differences" over how EFAC should be funded and the shape it should take.
"Richard and Caroline have done important and much needed work to revive international co-ordination of the many EFAC national fellowships who have maintained a continuous operation for many years and to establish new EFAC fellowships, for which we are thankful to them and to God," they said.
"Times of transition sometimes open up differences which can include differences about long term structure and funding and that has been the case here."
They added that there had been "no change of vision" about the aims of EFAC to "promote the supreme authority of Scripture" in the Anglican Communion and "share with members of the Anglican Communion a commitment to biblical obedience, particularly in the areas of Christian discipleship, servant leadership, church renewal, and mission in the world", among other objectives.
The EFAC Executive and Trustees said they hoped to announce the appointment of a new part-time honorary general secretary shortly.
Mr Crocker was appointed EFAC General Secretary in January 2018 and confirmed in the position during a meeting of the International Council in Nairobi last October.
Following his appointment, his wife Caroline, a scientist and writer, came onboard to manage EFAC's communications and online presence.
In their own statement, the Crockers said they had been "forced away" from their roles and that the decision had left them with "sad hearts".
"Over the past few months it has become evident that the EFAC Trustees do not share our vision for EFAC," they said.
"It was our intention to work towards fulfilling the goals set by the International Council, raise funds, and help EFAC to become a truly international community governed by the International Council."
They continued: "We have been asked to cease our volunteer service to EFAC. They have decided to move in a different direction. We are, of course, complying with that decision.
"It has been an enormous privilege to have spent the past year and a half working towards the redevelopment of the vital and strategic ministry of EFAC, as written in the EFAC Constitution.
"We are grateful to have seen such an outpouring of the Lord's blessing. We have loved having the opportunity to encourage and be encouraged by EFAC members around the world. We've enjoyed meeting you, getting to know you, and serving you.
"We hold each of you deep in our hearts and, frankly, are very sad to have been forced to step away from continuing to serve the extraordinary fellowship of which you are a part."
In a follow-up blog on Saturday, Caroline said she was "hurting a lot" over the decision not to renew their roles.
"It happened again. Life threw me an unexpected curve ball. I did nothing to deserve it. In fact, I truly believed that I deserved praise, not a push," she wrote.
"Friends tell me that they agree. I gave the work everything I had. What was worse, the push came from brothers in Christ. So, I'm hurting. A lot."
She concluded: "I am praying that what has happened to me will work out for the benefit of the Kingdom. Because my God is powerful and good, I'm confident that it will. And, because my life is safe in Christ, I'll be okay, too."