Tuna muscle is known to contain high levels of mercury, necessitating the monitoring of mercury concentrations in farmed fish at production sites. There is currently no straightforward in on-site method for testing whether the mercury levels in farmed tuna exceed regulatory limits. This study investigated the potential application of liquid asymmetric electrode plasma optical emission spectroscopy (LAEP-OES) to estimate mercury concentrations in the tissues of cultured Pacific bluefin tuna at aquaculture farms. No significant differences in mercury concentrations were observed between the ventricle tissue and biopsied tissue from tuna bleeding site (TTBS), which can be harvested without reducing the market value of farmed tuna (Hg concentration of the ventricle tissue and the TTBS, median: 0.41 and 0.40 mg/kg, respectively). In addition, the relationship between mercury concentrations in the ventricle tissue and in the edible portions of three tuna fish was examined. The findings showed that that total mercury level in the edible tissues varied, with the ratio of the mercury level in edible tissues to that in the ventricle ranging from 0.39 to 1.08. A positive correlation was observed between the average total mercury levels in edible tissues and ventricle tissue. These results suggest that determining the total mercury level in the ventricle, which is typically discarded at processing sites, may serve as a convenient proxy for quality control and monitoring purposes using the LAEP-OES method. However, larger sample sizes are needed to validate the proposed approach more robustly.