This article analyzes the creation, in 1914, of the prelature of Registro do Araguaia in Mato Grosso, Brazil. The government's indigenist policy intensified the disputes and tensions between the Church and State regarding management and guardianship of the Indigenous populations. Apostolic nuncio Giuseppe Aversa saw the situation as adverse to religious catechesis and considered the Salesian missions as the most threatened in Brazil. As a reactionary measure, he proposed a Holy See intervention to safeguard the presence of the Catholic Church among the Indigenous populations. This paper seeks to contribute to this debate by analyzing a set of diverse sources found in the Vatican Apostolic Archives, in the Archives of the Sacred Congregation of Extraordinary Ecclesiastical Works, and in the Hemeroteca Digital, which allowed us to understand the articulations, strategies and projects of the nuncio and the Holy See against the indigenist policy and the Indian Protection Service.