Hypophosphatasia (HPP) is a common inherited skeletal disease. Early exfoliation of primary teeth is known as a dental manifestation of HPP, and sometimes this symptom leads to a diagnosis of HPP. This study aimed to investigate the dental manifestations of HPP in the Japanese population, focusing on dentition and occlusion. A total of 609 dental clinics among general hospitals with dentistry departments were invited to participate. Clinics were sent questionnaires about the number of HPP cases encountered from 2018 to 2022. When clinics indicated that they had treated HPP cases, we proceeded with a second questionnaire about the clinical dental findings of these cases. A total of 103 clinical records of HPP from 30 clinics were collected. Forty percent of non-odonto type cases showed enamel hypomineralization, which was significantly higher than the incidence found in odonto type cases (8.5%) (P < 0.001). Non-odonto type cases also exhibited malocclusion (40.0%), poor oral habits (29.1%), and dysphagia (23.6%). The number of dental visits made by HPP patients is increasing because of the development of new treatments and increased disease awareness. Dental symptoms of HPP vary in severity, with particularly severe forms of HPP associated with enamel hypomineralization, malocclusion, poor oral habits, and dysphagia. Patients with HPP require not only medical collaboration but also multidisciplinary dental care according to the severity of the disease.