In this paper we present the findings of a case-study on IT system security in the area of EU internal security and justice. We have analyzed the implementation of information security for the EU information systems EURODAC, SIS II and VIS in case of Estonia. The analysis comes in a situation, where there are multiple regulations, directives, guidelines; but it lacks a unified standard for the implementation of the member states subsystems. The main finding is that a separate standard is not necessary; however, there is a need for setting minimum requirements, ensuring security of the information systems, that come with appropriate guidelines that help the member states to achieve the minimum requirements. The second finding is that there is a need for greater cooperation and an increased knowledge exchange of the methods used in the member states. Following defined guidelines and exchanging knowledge would help to strengthen the level of security for the entire system.