Phosphates are present on the surface of the Mio-Pliocene unconformity in the Otway, Port Phillip and Gippsland basins of south-east Australia. The phosphates occur as lenticular lag deposits and include reworked phosphatic intraclasts, vertebrate bone and teeth. In situ phosphatized burrows are also found in sediments of Late Miocene and Early Pliocene age. The phosphatic intraclasts on the unconformity are interpreted as reworked phosphatized burrows derived from latest Miocene sediments (6 to 5 Ma). The phosphatization of these intraclasts is temporally related to the unconformity. The timing of phosphogenesis coincides with a period of transgression across the south-east Australian margin following Late Miocene uplift. This transgression is responsible for initial marine erosion of the underlying Miocene sequence, creation of a period of very slow sedimentation that was favourable to phosphate formation and subsequent deposition of the latest Miocene through to Pliocene sediments. The continental weathering of the uplifted highlands adjacent to the sedimentary basins, global phosphorus enrichment in the Late Miocene oceans and localized upwelling may all have contributed to phosphatization in south-eastern Australia.