By 1817 Flaget was able to supply clergy to care for the French and Native American peoples living around the Great Lakes. He also began to establish parishes in Indiana and Michigan. In 1819 he proposed to the Sacred Congregation for the Propagation of the Faith (which oversaw the American Church as a missionary territory) the subdivision of his diocese. Eventually the diocese was subdivided, the first division becoming the Diocese of Cincinnati. Flaget was the principal consecrator of that new diocese's first bishop, Edward Dominic Fenwick, O.P. His counsel was also sought by the Congregation in international matters, such as resolving a dispute between the Canadian Sulpicians and the Archbishop of Quebec.