This study aimed to determine the challenges that cause a delay in the diagnosis of Japanese patients with specific intractable diseases by means of a survey. We conducted a questionnaire survey involving 424 patients with 12 specific intractable diseases. Pearson's chi-square test was used to examine the relationship between diagnostic delay and each factor. The reasons for the diagnostic delay were analyzed. Pearson's chi-square test showed statistically significant differences in the relationship between the period to definitive diagnosis and period between symptom onset and first hospital visit (p = 0.002), and the period when the patients suspected the disease (p < 0.001). Reasons for diagnostic delay of these patients were patients' time constraints, problem in access to medical institutions, hesitancy in seeking medical attention, and healthcare system issues. Early definitive diagnosis of intractable diseases was hindered by several important issues. The resolution of these issues will require combined societal efforts as well as improvements in the healthcare system. The study revealed the need for improving patients' awareness about their disease, enabling patients to be proactive towards achieving a definitive diagnosis, and making improvements in the healthcare system regarding early diagnosis and care of patients with intractable diseases.