Lucas Mangope, a local traditionalist who was later installed as a Bantustan leader, continued the practice of chiefly alliance with the mission, which had been established by earlier generations of chiefs. The close relationship the Hermannsburgers enjoyed with Mangope did not, however, characterise all relationships between the mission and the chiefs. Indeed, relationships were often tense and conflictual, and became increasingly so during the 1950s. Much of this conflict emerged in the preceding decades when local communities challenged chiefly authority on the grounds of financial mismanagement or efforts to extract levies from communities who belonged to the ethnic group but did not have any interest in the land, to pay for indebted land.

Particularly in the 1940s and 1950s, there is evidence that these conflicts spilled over into schooling. If in the earlier period conflict had centred within the ethnic group, in the later period the mission was identified as a problematic locus of authority alongside the chief. As schools became central to conflicts between communities, missionaries and chiefs, their authority was increasingly challenged and their position became more vulnerable. The chief inspectors of Native Education and the Native Affairs department were recruited by both sides in these battles and played a critical mediating role.

The Bantu Education Act (No. 47 of 1953) envisaged a removal of control from missionaries, not only to the state, but in rural areas also to local African communities linked with traditional authorities recognised by the state. While many African schools did have some form of school board or committee before the Act was passed, the Act now specified their composition: in rural areas two of their seven members were to be nominated by the secretary for Bantu Education to represent religious or other interests, while the rest were to be nominated by the tribal authority or by the chief subject to the secretary's approval. The ‘retribalisation’ purposes of the Act have been well-documented: to situate Africans ‘psycho-ideologically where the Bantustans placed them physically and politically’.