More than 3,150 lay and ordained members of the Church signed an open letter opposing the House of Bishops' transgender guidance.
Dr Ian Paul, member of Archbishops' Council, Archdeacon of Hastings Dr Edward Dowler, Church of England Evangelical Council and Fulcrum member, Rev Rachel Marszalek, and the Rev David Baker organised the letter.
They met with bishops and officials in London to raise their concerns.
Responding to the meeting, the delegation said in a statement: "The group was encouraged that the bishops agreed that the press release that accompanied the guidance had been unhelpful, and that they have undertaken to remove it from the Church of England website.
"We were further concerned that parish churches served by both ordained and lay signatories of the open letter had subsequently been collated and listed as ones that 'trans people and parents of trans children might want to think twice about attending'.
"We were glad that the bishops shared our concern for respectful public dialogue."
It was decided in December, 2018 that pastoral guidance produced by the House of Bishops Delegation Committee, whose chair Rt Rev Julian Henderson is president of the Church of England Evangelical Council, was to be incorporated into the Church's Common Worship library of service resources.
Ceremonies should allow transgender people to renew the commitment they made during their baptism service - prior to their gender transition - the guidance released said.
However, the delegation argued that "much more work needed to be done in relation to unexplored theological and pastoral ramifications of the guidance".
"We remain concerned, however, about what seems to us to be ill-considered use of the Bible in the guidance, as well as the apparent influence upon it of highly contested gender ideology," the delegation added.
"In the light of our concerns, we continue to believe that the guidance should be withdrawn, until such time as the Living in Love and Faith project is able to offer more considered reflection upon these crucial issues."
Despite wanting the guidance to be withdrawn, the delegation said they agreed on "the importance of welcoming transgender people to our churches".
"The gospel invitation to repent and believe the good news of Jesus is something for all people everywhere without exception," they went on to state.
"We would also all be delighted to assist all people to reaffirm their baptismal vows as an expression of their identity in Christ and their desire to live wholly for him.
"We are all sinners at the foot of the cross together; we all need and delight in the grace and unconditional love of God which we know we do not merit.
"We pray that through our flawed and fallible endeavours, and through our inevitably partial perspectives, God may be truly glorified."
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