Towards the beginning of 1993, following some basic modifications on the organizational structure of the Department conceived in 1988 after the merge, a new structure was established. A new procedure to formulate this structure was adopted, based on the practical follow-up of the daily work, and thus, allowed the early discovery of any needs for modification within the Department.

This led to the cancellation of several directorates and divisions. Other divisions were merged with new directorates, such as the Directorate of Internal Inspection and Monitoring

More importantly, the amendments that occurred on the old structure resulted in finding one assisting figure for civil status and passport issues, and another for the administrative and financial affairs. This was the direct result of the concept of merging the two departments, and considering them as one structure, both structurally and financially. The effect of decentralization was the delegation of all administrative and technical competences to the directors of directorates and their direct subordination to the Director General. In 2002, the organizational structure of the Department was modified in accordance with the needs of the policy of centralization in planning and decentralization in implementation. The organizational structure of the Department is horizontal, rather than vertical, which is very much in line with the social practices of the Arab society in general and the Jordanian society in particular. Indeed, the citizen wants to be able to communicate with the person in charge without going through different stages of decision-making before reaching the person required. Another advantage is the speed of decision-making, and without going through many administrative stages, thus leading to a better satisfaction of the citizen and less wasted time and energy.