CFM itu sendiri terdiri daripada 3 pertubuhan utama gereja di Malaysia iaitu; Catholic Bishops' Conference of Malaysia (CBCM), Council of Churches of Malaysia (CCM) dan National Evangelical Christian Fellowship (NECF).
Berikut ialah keanggotaan pertubuhan-pertubuhan gereja itu;
Council of Churches of Malaysia mewakili gereja-gereja berikut:
Anglican Diocese of Kuching
Anglican Diocese of Sabah
Anglican Diocese of West Malaysia
The Basel Christian Church of Malaysia
The Evangelical Lutheran Church in Malaysia
The Lutheran Church in Malaysia
Mar Thoma Syrian Church in Malaysia
The Methodist Church in Malaysia
The Methodist Church (Chinese Annual Conference)
The Methodist Church (Sarawak Chinese Annual Conference)
The Methodist Church (Sarawak Iban Annual Conference)
The Methodist Church (Tamil Annual Conference)
The Methodist Church (Trinity Annual Conference)
The Sabah Provisional Annual Conference
Orthodox Syrian Church
The Presbyterian Church in Malaysia
The Protestant Church in Sabah
The Salvation Army
National Evangelical Christian Fellowship mewakili gereja-gereja tersebut:
Assemblies of God
Baptist Church
Brethren Church
Evangelical Free Church
Full Gospel Assembly
Full Gospel Tabernacle
Hope of God Church
Independent Churches
Latter Rain Church
Sidang Injil Borneo Sabah
Sidang Injil Borneo Sarawak
Sidang Injil Semenanjung
