Pockmarks are morphological expressions of seabed fluid escape along continental margins. Identifying the underlying controls on their formation and spatial distribution is crucial for understanding substrate fluid plumbing systems and has important implications for hydrocarbon exploration, seafloor stability and seabed release of greenhouse gasses. Here, we use 3D seismic reflection dataset and a machine learning approach to present the first evidence for paleo-pockmarks in the Bass Strait, southeast Australia. The paleo-pockmarks are identified in the Bass Basin, within an interval between 250 and 310 m below present-day seafloor, corresponding to the Miocene carbonate-dominated Torquay Group. The paleo-pockmarks have depths ranging from ∼29 to 74 m and areas between ∼0.01 and 0.8 km2, with diameters varying between ∼0.1 and 1.1 km. The absence of an underlying seal-bypass system such as pipes and faults associated with these paleo-pockmarks discounts a deeper thermogenic source or a potential magmatic-driven fluid system. Rather a biogenic fluid system derived from the degradation of organic-rich layers and pore water expelled during early-stage compaction is hypothesised to drive paleo-pockmark formation. The seismic interval comprising these paleo-pockmarks demonstrates a distinctive seaward progradation and stepping-down configuration, indicating a forced regression. We propose this resulted in destabilization of hydrostatic pressure triggering the creation of the paleo-pockmarks.