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This study investigated how Japanese speakers interpret structurally ambiguous wh-questions, testing whether filler–gap resolution is guided by syntactic resolution based on hierarchical structure or linear locality based on surface word order. We combined behavioral key-press responses with fine-grained eye-tracking data and applied cluster-based permutation analysis to capture the moment-by-moment time course of syntactic interpretation as sentences were processed in real time. Key-press responses revealed a preference for resolving the dependency at the main clause (MC) gap position. Eye-tracking data showed early predictive fixations to the MC picture, followed by shifts to the embedded clause (EC) picture as the embedded event was described. These shifts occurred prior to the appearance of syntactic cues that signal the presence of an EC structure, such as the complementizer -to, and were therefore most likely guided by referential alignment with the linguistic input rather than by syntactic reanalysis. A subsequent return of the gaze to the MC picture occurred when the clause-final question particle -ka became available, confirming the interrogative use of the wh-phrase. Both key-press and eye-tracking data showed that participants did not commit to the first grammatically available EC interpretation but instead waited until clause-final particle information confirmed the interrogative use of the wh-phrase, ultimately favoring the MC interpretation. This pattern supports the view that filler–gap resolution is guided by structural locality rather than linear locality. By using high-resolution temporal data and statistically robust analytic techniques, this study demonstrates that Japanese comprehenders engage in predictive yet structurally cautious parsing. These findings challenge earlier claims that filler–gap resolution in Japanese is primarily driven by linear locality and instead showed a preference for resolving dependencies at the structurally higher MC position, consistent with parsing biases previously observed in English, despite typological differences in word order between the two languages. This preference also reflects sensitivity to language-specific morpho-syntactic cues in Japanese, such as clause-final particles.