To describe current neonatal pain management and individual and organizational factors that can improve neonatal pain practice from the viewpoints of both head nurses and head neonatologists in Japan. An anonymous questionnaire was sent to general perinatal maternal and child medical centres that had level 3 units across Japan. A total of 61 of 89 head nurses and 54 of 89 head neonatologists replied. The responses of head nurses and head neonatologists were almost the same. More than 60% of units (head nurses, 65%; head neonatologists, 61%) did not use pain scales, and about 63% units (both head nurses and head neonatologists) had no rules for health care professionals on the best methods for implementing pain relief for painful diagnostic and therapeutic procedures. Only 17% of head nurses and 24% of head neonatologists considered that nurses and physicians in their units collaborated in pain management, and <20% of units (both head nurses and head neonatologists) had written guidelines for their unit on neonatal pain management. This study suggested that Japanese neonatal intensive care units need national guidelines for pain management, and these might improve collaboration between nurses and physicians in minimizing neonatal pain.