In 1986 the Australian Catholic Bishops' Conference (ACBC) established a working party to examine the industrial relations needs of the Catholic Church in Australia.

This working party was formally recognised by the ACBC in 1987 with the establishment of the National Consultative Committee on Industrial Relations (NCCIR). The role of the NCCIR was to monitor the Church in its responsibilities as an employer and to identify the Church's requirements for industrial relations advice.

In 1989 the ACBC appointed a full time Secretariat to support the NCCIR. The Committee and its Secretariat commenced operation in January 1990 in Canberra. It was to formally report to the ACBC through the Bishops Committee for Industrial Affairs (BCIA).

In 1991 the NCCIR was renamed the "Australian Catholic Commission for Industrial Relations" (ACCIR) to give recognition to the work and status of the organisation.

In 1999 the ACCIR was renamed the "Australian Catholic Commission for Employment Relations" (ACCER) to give recognition to the wider scope and activities of the organisation in all matters affecting the employment relationship.

In 2001 to give recognition to the evolving nature of the work being undertaken and the future needs of the Catholic Church regarding employment relations matters, the ACBC mandated new Terms of Reference for the ACCER. This included the establishment of networks within each of the major sectors of Church activity - diocesan and parish administration, health and aged care, welfare and education. The networks enable the ACCER to elicit information about key employment relations issues and needs of Church organisations within each of the sectors and facilitate the sharing of information. 

In 2005, following a restructure of the Australian Catholic Bishops Conference, the Australian Catholic Commission for Employment Relations was renamed the Australian Catholic Council for Employment Relations and became an advisory body on matters of national employment relations matters to the ACBC through the Bishops Commission for Administration and Information.