Generating accurate estimates of the number of vessels in fishing ports using traditional methods (i.e., ground- and boat-based) can be challenging as observations are distorted by an horizontal perspective. Automated inspection using drones is an emerging research alternative for this type of investigation. However, the drone-based and ground- and boat-based survey methods have not been quantitatively compared for small-scale and commercial fishing fleets in their ports. The objective of this study was to determine the number of fishing vessels and detect onboard fishing gear using three independent sources of data along 41 ports across the Brazilian coastline. Proved by statistical significance, the drone-derived vessel counts revealed 17.9% and 26.6% more fishing vessels than ground- and boat-based surveys, respectively. These differences were further highlighted during the assessment of ports without a ground walkway, causing difficulty, especially for ground-based surveys. Considerable numbers and types of onboard fishing gear were detected using the drone survey, that could not be detected using the ground- and boat-based methods. Although the ground-based survey was associated with a lower cost in comparison with other methods, the drone-based survey required the least time to record fishing fleet features in study ports. Our findings demonstrate that drone surveys can improve the detection and precision of counts for fishing vessels and fishing gear in ports. Further, the magnitude of the discrepancies among the three methods highlights the need for employing drone surveys as a considerable time-reducing approach, and a cost-effective technique for fishery studies.