An object control and tracking system and related methods using separate object identification and location detection mechanisms for objects, such as keys, that are maintained in a secure enclosure, such as a key drawer. A plurality of object slots are located on the top tray of the enclosure to receive object tags that include both an RFID tag and an object to be tracked. The objects (e.g., keys) are attached to a portion of the object tags that are outside of the enclosure. Presence detectors are used to determine if an object tag is present in the corresponding slot of the enclosure. RFID sensors located on opposite interior side walls of the enclosure interrogate each RFID tag to determine the presence of each RFID tag within the enclosure. The object control and tracking system includes a controller, a memory for storing an object control database, and related processing logic operating on the controller to control scanning of the presence detectors to determine an object tag's presence in a corresponding slot, to identify each object present in the enclosure and to compare the identified objects with an object control database to determine each object removed or replaced since the previous database update.