The church was built in 1849 on the site of an old Portuguese Church of St Dominic by a French MEP priest, Father Farvé. Fr. Farvé was sent to as far as the South Americas to raise funds for the church in which was finally enough in 1856. The finishing touches of the building were completed in 1856 by Father Allard, with the present-day presbytery built in 1874. The church's origins actually dated from 1845 but was not successful due to jurisdiction issues with the Portuguese's
St. Peter's Church (Melaka) which was under the administration of the diocese of
Macau. In the early 1900s, a marble high altar was purchased from France and placed in the sanctuary. It was once known as one of the most stunning altar pieces in the region, and now forms part of the current altar after the redesigning of the sanctuary during the
Vatican II process. Much of the church remains unchanged except for the portico added in 1965 and building of a shrine in front of the church a few years after. The Church of St Francis Xavier is also known to found numerous other parishes within the
Roman Catholic Diocese of Malacca–Johor such as
St. Philip's Church, Segamat,
St. Theresa's Church (Melaka), St Andrew Church Muar in 1908 and St Mary Ayer Salak in 1848. ==Architecture==