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Recent advances in biotelemetry techniques, especially positioning methods, have revealed the detailed behaviour and movement of aquatic organisms. Behavioural intermittence in animal locomotion, such as the Lévy walk, is a popular topic in the field of movement ecology. Previous attempts to describe intermittent locomotion quantitatively have been constrained by the spatial and temporal resolution possible with conventional biotelemetry systems. This study developed a fine-scale spatiotemporal three-dimensional positioning method using a new biotelemetry system with a positional precision of <10 cm and positioning interval of <10 s. Using this proposed positioning method, the intermittent stop-and-go locomotion of Siebold’s wrasses (Pseudolabrus sieboldi) was observed during travel from an unsuitable to a suitable location following displacement. The fish displayed behavioural intermittence in relocating to a suitable location. Initially, their movement halted for reorientation, after which they moved intermittently yet in a straight line to the suitable location. To test the positioning ability of the proposed method, data sets were resampled at intervals of 5, 10, 30, 60, and 300 s. Longer sampling intervals failed to identify reorientations and underestimated the number of stops, distance travelled, and speed. Overall, the results highlighted the adequacy and ability of the proposed positioning method to observe the intermittent locomotion of fish, such as stop-and-go behaviour, in a natural environment.