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First Nations were compelled to take back control of education in the historic Wahbung paper of 1971 – Wahbung: Our Tomorrows – by the Manitoba Indian Brotherhood (now Assembly of Manitoba Chiefs) and Indian Control of Indian Education position paper in 1972 by the National Indian Brotherhood (Now Assembly of First Nations).

Therefore, at that time and beyond, First Nations began the process of administering their own schools; however, chronic underfunding and lack of supports eventually required the creation of an organization that could help meet the needs of those schools.

In 1998 the Assembly of Manitoba Chiefs gave a mandate and established MFNERC to provide administrative, technical, language and educational supports to First Nations Schools in Manitoba.

In May of 2000 in Opaskwayak Cree Nation and 2006 in Dakota Tipi First Nation, the Chiefs-in-Assembly of the AMC passed a resolution to provide ongoing support for MFNERC.

In June, 2012, the AMC amended the mandate of the Centre to offer enhanced second level services (school division-type services) while moving towards the development of First Nations Education Systems. All services continue to be based on needs as identified by the First Nation, and MFNERC continues to be governed by the AMC with the authority remaining with the First Nations.