Physical contact is frequently used as a pedagogical tool in sports instruction. However, it may elicit discomfort owing to factors such as gender dynamics, relationship type, and contacted body parts. This study investigated how gender, relational closeness, and specific body parts influence the perceived discomfort of physical contact in sports-related scenarios. A within-subject questionnaire survey was administered to female university students in Japan. Participants rated the discomfort level of hypothetical physical contact scenarios involving the same sex or opposite sex, three relational contexts (close friend, unfamiliar friend, and teacher), and 11 body parts. Logistic regression and generalized estimating equations analyses revealed significant main effects for all three factors and significant two-way interactions. Notably, contact from male individuals, less close acquaintances, or male teachers evoked the highest discomfort. These findings support the intimacy congruence hypothesis, suggesting that comfort with physical contact depends on both the body part and the social congruity between initiator of contact and recipient of contact. Although physical contact may be normatively justified in sports coaching, complex social cues significantly shape reception. These findings highlight the importance of gender sensitivity and relational dynamics in physical instruction and suggest that educators should exercise nuanced judgment when using contact as a pedagogical method.