The study investigates the correlation between prosodic patterns and epistemic bias observed in Japanese negative polar interrogatives, with special attention given to the perceptual and functional aspects of the correlation. The result of a naturalness rating test and a comprehension test demonstrate that listeners perceive the matching interrogative-answer pairs more natural, compared to the conflicting pairs. Also, it is revealed that the prosodic patterns successfully guide listeners to identify the epistemic bias of negative polar interrogatives.