Main objective of this research is to develop the existing fingerprint authentication system implemented in AOU Bahrain which automatically uses only fingerprints matching between measured & reference template minutia stored in database for validating identity of employee. Modified Employee authentication System suggest adding more security measures which are facial and smart card (RFID tag) to be scanned by car park barrier sensor when employee entering and leaving car park also same smart card to be swiped in case employee entering & leaving university by walking in order to increase system security. Modified system is designed to ensure that the organization is equipped with the high level of human resource tracking for each separate department of the organization. The main feature of Employee authentication System is time tracking for employees. The system is integrated and implemented with biometric facial & fingerprint features that identifies certain or specific employee as well as possess of smart card. The system can be accessible from remote network. The developed system also includes the employee fingerprint and facial verification, employee attendance, employee tracking, employee leave, and salary payment modules. The operational activities of the system are accessed or controlled by IT service department, also the research work is concerned with the study of security & errors of actual existing biometric fingerprint authentication system implemented in AOU Bahrain compared to suggested modified combined method which implements fingerprint, facial and smart card (RFID tag).