The PRAYER COMMISSION aims at stimulating a national prayer movement among churches, through seminars, consultations, and prayer mobilization programmes.

The EVANGELISM COMMISSION assists churches to strategize ways to fulfill the Great Commission, through consultations, research, and documentation of information related to mission and evangelism.

The LEADERSHIP COMMISSION helps churches to develop emerging leaders, revitalize plateau leaders and restore wounded or burnt-out leaders through relevant programmes devised by the commission and/or though collaboration with other ministries.

The RESEARCH COMMISSION studies, monitors, and interprets the spiritual significance of past, contemporary and emerging issues and provides appropriate responses to help Christians to be watchful, prayerful, and proactive.

The RELIGIOUS LIBERTY COMMISSION monitors the state of religious liberty climate in our country and presents annual reports to the NECF's council which are subsequently published and made available to our members and others.

YOUTHNET provides a platform for interactions between youth ministries, serves churches in the growth needs of their youth fellowships or youth groups, researches on issues related to working with youths and represents Christian Youth Ministries in engagements with the government.

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The TAMIL COMMISSION seeks to motivate Tamil churches to work together to overcome the composite and contextual challenges in fulfilling the Great Commission among the Indian peoples of our nation.

The WOMEN COMMISSION aims to raise the profile, contributions and concerns of Christian women in Malaysia through networking with churches and organizations.

The ORANG ASLI (OA) COMMISSION - the indigenous peoples of Peninsular Malaysia.