Whale meat products sold on Japanese markets originate from two stocks of North Pacific (NP) minke whales Balaenoptera acutorostrata scammoni: the depleted J-stock, which has been protected since 1986 but continues to be killed as fisheries ‘bycatch’, and the more abundant O-stock, which is hunted under special permit (scientific whaling). We investigated the geographic distribution and temporal changes in stock composition of NP minke whale products sold on Japanese markets between December 1997 and June 2004. From nearly 1200 ‘whale meat’ products purchased during this time, 250 were identified as NP minke whales by phylogenetic analysis of mitochondrial DNA (mtDNA) sequences. The 250 NP minke whale products were found to represent 201 unique ‘market individuals’ after exclusion of replicate products using microsatellite genotypes. Market individuals were further classified into four mtDNA haplogroups, three of which are characteristic of the J-stock (J-type) and one characteristic of the O-stock (O-type). There were moderate differences in the proportions of J-type individuals found in coastal prefectures, perhaps reflecting regional differences in the sale of local bycatch, but no significant difference across time. The absence of a change over time was inconsistent with the four- to fivefold increase in reported bycatch, from an average of 25–122 whales year−1, following a 2001 regulation allowing commercial sale of whales taken as bycatch. Using a mixed-stock analysis based on haplogroup frequencies over the entire survey period, we estimated that 46.1% (se, 4.2%) of all market individuals originated from the J-stock. This estimate of illegal, unreported or unregulated (IUU) exploitation is higher than expected from the officially reported bycatch, suggesting either large-scale under-reporting and/or unrecognized takes of J-stock minke whales from Pacific coastal waters by the scientific hunt. Our estimates of the true level of IUU exploitation have important implications for recovery of this depleted coastal stock.