Little provision had been made in the original church for the clergy. A room for the priest was provided up a narrow winding staircase to the left of the apse and behind St. Thomas’ chapel. The sacristy was under the former mission church and accessible from a door in the ambulatory.

When the Chapel of St. Francis was adapted in 1990 to become the sacristy, the arches were filled in between the south passage aisle and the chapel itself. The chapel comprises four high bays with Soanian vaulting with piers on which stylised angels are carved. There is a lower bay to the west, separated by glass panels, which is the confessional area. Above the Altar at the east end is a pair of lancet windows with figures of St. Francis on the left and St. Chiara (Clare) on the right. In the roof are glazed oculi.

The sacristy has its own altar of kauri pine, a tabernacle and also a crucifix modelled on an Italian pattern of the 16th century.