Methods of operation for data reader and security tag deactivation system whereby a data reader is equipped with EAS deactivation coils/modules disposed in the vicinity of the read volume or generally proximate thereto. System is operable to permit reading of the ID tag on an item, and upon a successful read, the deactivation unit is operable to (1) sense presence of an EAS tag; (2) if presence of EAS tag is sensed, energize the deactivation coil/module to deactivate the EAS tag; (3) sense if EAS tag is deactivated. If EAS tag is sensed to have been deactivated, the system signals and next item is scanned. Also, it may be operable to urge the operator to return an item to the read volume to enhance EAS tag deactivation, one method being by delaying good read acknowledgment until determining that the EAS tag which may have been previously detected has subsequently been deactivated.