Abstract We describe the first ever implementation of a clock-based, multi-stage emulsion shifter in an accelerator neutrino experiment. The system was installed in the neutrino monitoring building at the Japan Proton Accelerator Research Complex as part of a test experiment, T60, and stable operation was maintained for a total of 126.6 days. By applying time information to emulsion films, various results were obtained. Time resolutions of 5.3–14.7 s were evaluated in an operation spanning 46.9 days (yielding division numbers of 1.4–3.8 $\times10^{5}$ ). By using timing and spatial information, reconstruction of coincident events consisting of high-multiplicity and vertex-contained events, including neutrino events, was performed. Emulsion events were matched to events observed by INGRID, one of the on-axis near detectors of the T2K experiment, with high reliability (98.5%), and hybrid analysis of the emulsion and INGRID events was established by means of the multi-stage shifter. The results demonstrate that the multi-stage shifter can feasibly be used in neutrino experiments.