This study aims to identify the sources and magnitude of uncertainty in the collection and processing of catch and effort data of small- and medium-scale tuna fisheries in Indonesia, as well as the causes of uncertainty on an operational level. We identified possible sources of uncertainty through a literature review and interviews with experts. Next, we surveyed 40 small-scale (<10 GT) and medium-scale (10–100 GT) pole-and-line, purse-seine, longline and handline fishers in the oceanic fishing port Bitung, which has the largest number of tuna fisheries activities in eastern Indonesia, to estimate the magnitude of unreported catch of juvenile tuna, on-board consumption, home consumption and catch used as bait. We used logbook data from the fisheries submitted to the fishing port authorities to extrapolate survey results to the fishing port level. Uncertainties around unreported catches were due both to non-reporting by fishers to the fishing port authority and to flaws in data management in the data collection institution. After removing flaws in the logbook database we estimated that the catch by small- and medium-scale fishing vessels active in Indonesian waters could be about 33–38% higher than reported. The proportion of unreported catch, as well as the sources and range of uncertainty, varied according to the types of gear used. Finally, we discuss what aspects of data collection and processing should be improved at the fishing port level, including the identified sources of unreported catch and the processes leading to non-reporting. We hence provide a methodology for estimating unreported catches in small and medium-scale fisheries.