Physicians’ not entering their patients can jeopardize the success of a randomized controlled trial (RCT). We used a survey to investigate the possible reasons why physicians who initially agreed to collaborate did not recruit any patients for an RCT being conducted in Japan. A total of 167 questionnaires were sent out and 122 responses were received. Main reasons for not entering patients were: concern about the detrimental effects on the doctor-patient relationship (51.8%), patients’ refusal (47.5%), complicated registration and follow-up procedures (34.9%), and not feeling comfortable recruiting their own patients (32.4%). Multivariate logistic regression made it clear that physicians who thought that registering their own patients would damage the doctor-patient relationship and who expected the RCT would fail were more likely to be uncomfortable entering their own patients. Moreover, physicians aged 50 years or older, who felt uncomfortable recruiting their own patients, and saw no advantage in participating in the trial, were more likely to view the enrolment and follow-up procedures as cumbersome. We conclude that training and a manual for obtaining informed consent and a face-to-face demonstration of patient registration/follow-up procedures for the potential participants are prerequisites for increasing physician participation in RCTs in Japan.