An on-vehicle apparatus control system includes: an on-vehicle control device; and a portable machine. The on-vehicle apparatus control system includes: a mode switching unit that selects a permission mode or a prohibition mode; and an illegality recording portion that records transmission or reception of a response request signal as illegality history in a case where the response request signal is transmitted from the on-vehicle control device or is received by the portable machine during the prohibition mode. If the response request signal is received by the portable machine during the permission mode, the portable machine transmits the response signal. If the response request signal is received by the portable machine during the prohibition mode, the portable machine transmits an illegality notification signal instead of the response signal, and the on-vehicle control device does not control an on-vehicle apparatus if the illegality notification signal is received.