With the increasing demand for tuna product and the dwindling resources, promoting sustainable measures is a must. Illegal, unreported, and unregulated (IUU) fishing is a damaging problem because it affects fisheries stocks. We identified the level of IUU fishing, particularly the underreporting of tuna catch, in the Philippines, and also the drivers and implications to the technical efficiency (TE) performance of fishing vessels. Samples were from General Santos City. Two data sets were gathered: an annual panel data of reported inputs and catch level of 216 registered fishing vessels at the Fish Port Authority and primary data involving 40 handline fishers. The latter data were compared to the former data set. It revealed underreporting by 51%−100% and is more prevalent in smaller vessels. Using stochastic frontier analysis, the TE scores of the tuna vessels were overestimated to 0.80, 0.70, and 0.72 using the panel data while the primary data set suggested a lower TE score of 0.66. This implies that the efficiency performance of the handline fishers could be lower by 6% if reporting were correct. We recommend increasing penalties for IUU fishing, increasing frequency of monitoring activities, and promoting an enabling environment for small-scale fishers