Disclosed is a tablet packaging controller of an automatic tablet packaging machine for recognizing information of tablets accommodated in tablet cassettes and tracking positions of the tablet cassettes. The controller includes RF tags recording tablet information, and tablet information access units receiving the tablet information via a wireless line, to transmit tablet information and identification information of cartridges to a host terminal, or to record new tablet information in the RF tags. The host terminal creates and stores position arrangement information of the tablet cassettes, estimates a quantity of remaining tablets, controls tablets to be discharged in a certain order of tablet cassettes, and controls the tablet information access units to package only the accommodated tablets when the remaining tablets are short, and displays the short tablet on an LCD, and controls the tablet information access units to package the remaining tablets when the short tablets are supplemented.