Although a community-based medicine program is a mandatory component of Japan’s postgraduate clinical training system, the employment status of residents during this period varies depending on each university hospital’s policies. We conducted an online survey of 126 university hospitals participating in the national residency matching program in Japan. The survey focused on the employment conditions of residents during their community-based medicine rotations. Of the 126 hospitals contacted, 56 (44%) responded. Nearly all reported that residents remained employed throughout the program, even when stationed at external medical institutions. Labor relationships during the rotation were categorized as secondment (24%), business trips (20%), and training (54%). Notably, 27% of hospitals indicated that overtime pay was provided by the partnering facility, even in cases involving labor-related work such as business trips or training. These findings suggest potential mismatches between attendance supervision and allowance payment responsibilities, which may pose certain risks.