A facilities-group system designed to provide clinical training at dental clinics was developed after postgraduate clinical training became mandatory for dentists in Japan in 2006. As a result, there has been a steady increase in the number of dental clinics collaborating with dental school hospitals under this program. A larger number of dental clinics have also been designated as single-system facilities, program management facilities or collaborating facilities. However, it remains to be determined whether this increase in the number of dental clinics designated as clinical training facilities has led to an increase in the amount of training offered. Therefore, the purpose of this study was to investigate trends in the percentage of postgraduate dental trainees at dental clinics between fiscal years 2006 and 2010. The results showed no significant correlation among (1) the percentage of dental clinics designated as single-system collaborating facilities, (2) the percentage of training programs at dental clinics, and (3) the proportion of training program recruitment offers by dental clinics compared to the total number of recruits. These findings showed that increasing the number of collaborating dental clinics did not lead to an increase in the amount of clinical training at dental clinics. The findings also suggest that increasing the number of single-system or program management dental clinics is important in promoting clinical training at dental clinics.