Vailankanni was a part of the parish of Nagapattinam, but as pilgrims began to pour into Vailankanni, it was raised to the status of an independent parish in 1771, and Fr. Antonio de Rozario the last parish priest of the Church of the Immaculate Conception, Nagapattinam, was appointed the first Parish priest of Vailankanni. Nagapattinam had always been under the ecclesiastical jurisdiction of the Bishop of the Diocese of Mylapore. During that period the Diocese of Mylapore was administered under the Portuguese 'Padroado' (patronage). Under the Padroado system, the king of Portugal in Europe met all the expenses incurred by the Diocese of Mylapore, which remained under the ecclesiastical jurisdiction of the Roman Pontiffs.
Until 1847 the priests of St. Franciscan Missionaries who had looked after the province of Goa and Mylapore also looked after Nagapattinam and Vailankanni. The Franciscan origin and ownership of the Shrine was also perpetuated, by giving the place of honor to two Franciscan saints, St. Anthony of Lisbon and St. Francis of Assisi, on either side of the miraculous image of 'Our Lady', on the High Altar until 1961. Besides the last parish priest, Miguel Francisco Fernandez, who was of the Franciscan order, controlled the parish of Vailankanni till 1889. In 1890 the parish was handed over to diocesan priests.
Thereafter, the diocesan priests of the Diocese of Mylapore were in charge of Vailankanni. In 1952, when the new Diocese of Thanjavur came into being, and Vailankanni became a part of the new diocese, the priests of Thanjavur Diocese became the custodians of the Shrine. The administration of the new Diocese was imagesorarily placed under the apostolic administration of the Rt. Rev. Dr. Louis Mathias, S.D.B., who was then the Archbishop of the new Archdiocese of Madras-Mylapore.
On March 19, 1953, His Excellency the Rev. Dr. R. Arokiasamy Sundaram, DD., L. C. L., M. A., a priest of Mylapore Archdiocese was appointed as the first Bishop of the new Diocese of Thanjavur. He assumed charge of his Diocese on March 24, 1953.
Vailankanni being situated in the Thanjavur District came under the jurisdiction of the Diocese of Thanjavur. The Rev. Dr. R. Arokiasamy Sundaram showed keen interest in the development of Vailankanni Shrine and granted special spiritual privileges. 'Our Lady of Health Vailankanni' became the second patroness of our newly erected Diocese.