The demand for autonomous nasopharyngeal swab sampling robot systems is increasing owing to the recent outbreak of the respiratory virus pandemic. To protect the medical staff from infection, automatic upper respiratory sample collecting robotic systems are needed. The nasopharyngeal swab sampling robot proposed in this study is composed of a unique force restriction mechanism, a precise 3-axis force sensor, and a compact remote center of motion (RCM) mechanism, which are designed to enhance safety and efficiency. The proposed force restriction mechanism has a constant repulsive force finely adjustable using specially designed leaf spring structures. The force sensor is a capacitance-type 3-axis force sensor based on flexure mechanisms. Owing to the RCM mechanism, the distal end of the swab remains stationary. The effectiveness of the proposed robot was verified by various experiments, including restriction force measurement and a sampling success rate test.