A new species of phocoenid cetacean Haborophocoena, collected from the Early Pliocene Embetsu Formation, in the close vicinity to the site where the holotype of the type species of the genus Haborophocoena was retrieved, improves our knowledge of the anatomy of this cetacean. The new species, represented by a skull, lacking distal half of the rostrum, ear bones, and teeth, is significantly smaller than, but morphologically similar to, the type species Haborophocoena toyoshimai Ichishima and Kimura 2005. This new record of Haborophocoena confirms the veracity of the genus Haborophocoena as a biological entity, contributes to understanding the interspecific variation, and suggests that the genus diversified in the northwestern Pacific of early Pliocene time. The adult-like degree of ossification in this small skull precludes it from being a juvenile of Haborophocoena toyoshimai. Autapomorphies of Haborophocoena minutus include narrow premaxilla on the dorsal surface of the rostrum, the anterior position of the premaxillary foramen, and a distinct ridge dividing a fossa on the lateral face of the base of the zygomatic process into the dorsal and the ventral halves, the zygomatic process rectangular in lateral profile, and its small size, which is the most compelling feature, making it a distinct species.