Perth Canyon Marine Park was established due to its regional significance for high biological productivity and aggregations of marine life, and as Australia’s largest submarine canyon. It is host to arguably the largest foraging aggregation of pygmy blue whales Balaenoptera musculus brevicauda in Australian waters. This work describes the foraging behaviour of pygmy blue whales in and around the Marine Park to assess the extent of foraging habitat and identify outstanding threats that are not adequately mitigated in the current management framework. We utilised tag datasets collected between 2002 and 2026 that include biologgers recording location and depth integrated feeding behaviour (n = 14), as well as location-only satellite transmitters (n = 19). The spatial distribution of presence and feeding effort was mapped in relation to the marine park zoning, geological features, diel patterns, ship strike risk, and spatial autocorrelation of the tag tracks. Shipping data was transformed to a risk factor based on vessel draught and speed. Daily patterns of deep diurnal feeding and shallow nocturnal resting indicated higher risk of ship strike at night. New mitigation measures for the risk of ship strikes on pygmy blue whales in the Perth Canyon Marine Park should be considered.