Marine predators feeding on fisheries catches directly on the fishing gear, a behaviour termed “depredation”, has emerged as a major human-wildlife conflict globally, often resulting in substantial socio-economic and ecological impacts. This study investigated the extent of this conflict in commercial Patagonian toothfish (Dissostichus eleginoides) fisheries across subantarctic waters where both killer whales (Orcinus orca) and sperm whales (Physeter macrocephalus) feed on toothfish caught on longline hooks. Using long-term datasets from six major fishing areas, from southern Chile to the Indian Ocean sector of the Southern Ocean, statistical models were developed to quantify the catch removals due to whale depredation interactions. The results indicated that these removals were large, totalling more than 6600 t of toothfish between 2009 and 2016 with an annual mean of 837 t [95% CI 480–1195 t], comprised of 317 t [232–403 t] and 518 t [247–790 t] removed by killer whales and sperm whales, respectively. Catch removals greatly varied between areas, with the largest estimates found at Crozet, where on average 279 t [179–379 t] of toothfish per year, equivalent to 30% [21–37%] of the total catches. Together, these findings provide metrics to assess the impacts of depredation interactions on the fishing industry, whale populations, fish stocks and associated ecosystems. With an estimated $15 M USD worth of fish depredated every year, this study highlights the large geographic scale and economic significance of the depredation issue and its potential to compromise the viability of some toothfish fisheries which are the primary socio-economic activity in subantarctic regions.