In early 1871, tension builds between Bishop Laurence Sheil, Father Julian and some priests who are determined to destroy the fledgling Sisters of Saint Joseph. The priests present a submission to Bishop Sheil highly critical of the sisters and Father Julian. Mary writes to the Bishop explaining her position.
On 22 September, at the Franklin Street Chapel in Adelaide, South Australia, Mary is excommunicated from the Church by Bishop Sheil, with many sisters being expelled. Five months later, on 23 February 1872, a very ill and sorrowful Bishop Sheil removes the excommunication of Mary, admitting he was misled by bad advisers. He dies on 1 March 1872. The sisters are restored to their habits on 19 March.